diff --git a/pyproject.toml b/pyproject.toml
index fc4b306351..dae79b0f6a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,6 @@ packages = ["src/specify_cli"]
 [tool.hatch.build.targets.wheel.force-include]
 # Bundle core assets so `specify init` works without network access (air-gapped / enterprise)
 # Page templates (exclude commands/ — bundled separately below to avoid duplication)
-"templates/agent-file-template.md" = "specify_cli/core_pack/templates/agent-file-template.md"
 "templates/checklist-template.md" = "specify_cli/core_pack/templates/checklist-template.md"
 "templates/constitution-template.md" = "specify_cli/core_pack/templates/constitution-template.md"
 "templates/plan-template.md" = "specify_cli/core_pack/templates/plan-template.md"
diff --git a/scripts/bash/update-agent-context.sh b/scripts/bash/update-agent-context.sh
deleted file mode 100644
index 2f71bb893c..0000000000
--- a/scripts/bash/update-agent-context.sh
+++ /dev/null
@@ -1,857 +0,0 @@
-#!/usr/bin/env bash
-
-# Update agent context files with information from plan.md
-#
-# This script maintains AI agent context files by parsing feature specifications 
-# and updating agent-specific configuration files with project information.
-#
-# MAIN FUNCTIONS:
-# 1. Environment Validation
-#    - Verifies git repository structure and branch information
-#    - Checks for required plan.md files and templates
-#    - Validates file permissions and accessibility
-#
-# 2. Plan Data Extraction
-#    - Parses plan.md files to extract project metadata
-#    - Identifies language/version, frameworks, databases, and project types
-#    - Handles missing or incomplete specification data gracefully
-#
-# 3. Agent File Management
-#    - Creates new agent context files from templates when needed
-#    - Updates existing agent files with new project information
-#    - Preserves manual additions and custom configurations
-#    - Supports multiple AI agent formats and directory structures
-#
-# 4. Content Generation
-#    - Generates language-specific build/test commands
-#    - Creates appropriate project directory structures
-#    - Updates technology stacks and recent changes sections
-#    - Maintains consistent formatting and timestamps
-#
-# 5. Multi-Agent Support
-#    - Handles agent-specific file paths and naming conventions
-#    - Supports: Claude, Gemini, Copilot, Cursor, Qwen, opencode, Codex, Windsurf, Junie, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Qoder CLI, Amp, SHAI, Tabnine CLI, Kiro CLI, Mistral Vibe, Kimi Code, Pi Coding Agent, iFlow CLI, Forge, Goose, Antigravity or Generic
-#    - Can update single agents or all existing agent files
-#    - Creates default Claude file if no agent files exist
-#
-# Usage: ./update-agent-context.sh [agent_type]
-# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic
-# Leave empty to update all existing agent files
-
-set -e
-
-# Enable strict error handling
-set -u
-set -o pipefail
-
-#==============================================================================
-# Configuration and Global Variables
-#==============================================================================
-
-# Get script directory and load common functions
-SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-source "$SCRIPT_DIR/common.sh"
-
-# Get all paths and variables from common functions
-_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
-eval "$_paths_output"
-unset _paths_output
-
-NEW_PLAN="$IMPL_PLAN"  # Alias for compatibility with existing code
-AGENT_TYPE="${1:-}"
-
-# Agent-specific file paths  
-CLAUDE_FILE="$REPO_ROOT/CLAUDE.md"
-GEMINI_FILE="$REPO_ROOT/GEMINI.md"
-COPILOT_FILE="$REPO_ROOT/.github/copilot-instructions.md"
-CURSOR_FILE="$REPO_ROOT/.cursor/rules/specify-rules.mdc"
-QWEN_FILE="$REPO_ROOT/QWEN.md"
-AGENTS_FILE="$REPO_ROOT/AGENTS.md"
-WINDSURF_FILE="$REPO_ROOT/.windsurf/rules/specify-rules.md"
-JUNIE_FILE="$REPO_ROOT/.junie/AGENTS.md"
-KILOCODE_FILE="$REPO_ROOT/.kilocode/rules/specify-rules.md"
-AUGGIE_FILE="$REPO_ROOT/.augment/rules/specify-rules.md"
-ROO_FILE="$REPO_ROOT/.roo/rules/specify-rules.md"
-CODEBUDDY_FILE="$REPO_ROOT/CODEBUDDY.md"
-QODER_FILE="$REPO_ROOT/QODER.md"
-# Amp, Kiro CLI, IBM Bob, Pi, Forge, and Goose all share AGENTS.md — use AGENTS_FILE to avoid
-# updating the same file multiple times.
-AMP_FILE="$AGENTS_FILE"
-SHAI_FILE="$REPO_ROOT/SHAI.md"
-TABNINE_FILE="$REPO_ROOT/TABNINE.md"
-KIRO_FILE="$AGENTS_FILE"
-AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
-BOB_FILE="$AGENTS_FILE"
-VIBE_FILE="$REPO_ROOT/.vibe/agents/specify-agents.md"
-KIMI_FILE="$REPO_ROOT/KIMI.md"
-TRAE_FILE="$REPO_ROOT/.trae/rules/project_rules.md"
-IFLOW_FILE="$REPO_ROOT/IFLOW.md"
-FORGE_FILE="$AGENTS_FILE"
-
-# Template file
-TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
-
-# Global variables for parsed plan data
-NEW_LANG=""
-NEW_FRAMEWORK=""
-NEW_DB=""
-NEW_PROJECT_TYPE=""
-
-#==============================================================================
-# Utility Functions
-#==============================================================================
-
-log_info() {
-    echo "INFO: $1"
-}
-
-log_success() {
-    echo "✓ $1"
-}
-
-log_error() {
-    echo "ERROR: $1" >&2
-}
-
-log_warning() {
-    echo "WARNING: $1" >&2
-}
-
-# Track temporary files for cleanup on interrupt
-_CLEANUP_FILES=()
-
-# Cleanup function for temporary files
-cleanup() {
-    local exit_code=$?
-    # Disarm traps to prevent re-entrant loop
-    trap - EXIT INT TERM
-    if [ ${#_CLEANUP_FILES[@]} -gt 0 ]; then
-        for f in "${_CLEANUP_FILES[@]}"; do
-            rm -f "$f" "$f.bak" "$f.tmp"
-        done
-    fi
-    exit $exit_code
-}
-
-# Set up cleanup trap
-trap cleanup EXIT INT TERM
-
-#==============================================================================
-# Validation Functions
-#==============================================================================
-
-validate_environment() {
-    # Check if we have a current branch/feature (git or non-git)
-    if [[ -z "$CURRENT_BRANCH" ]]; then
-        log_error "Unable to determine current feature"
-        if [[ "$HAS_GIT" == "true" ]]; then
-            log_info "Make sure you're on a feature branch"
-        else
-            log_info "Set SPECIFY_FEATURE environment variable or create a feature first"
-        fi
-        exit 1
-    fi
-    
-    # Check if plan.md exists
-    if [[ ! -f "$NEW_PLAN" ]]; then
-        log_error "No plan.md found at $NEW_PLAN"
-        log_info "Make sure you're working on a feature with a corresponding spec directory"
-        if [[ "$HAS_GIT" != "true" ]]; then
-            log_info "Use: export SPECIFY_FEATURE=your-feature-name or create a new feature first"
-        fi
-        exit 1
-    fi
-    
-    # Check if template exists (needed for new files)
-    if [[ ! -f "$TEMPLATE_FILE" ]]; then
-        log_warning "Template file not found at $TEMPLATE_FILE"
-        log_warning "Creating new agent files will fail"
-    fi
-}
-
-#==============================================================================
-# Plan Parsing Functions
-#==============================================================================
-
-extract_plan_field() {
-    local field_pattern="$1"
-    local plan_file="$2"
-    
-    grep "^\*\*${field_pattern}\*\*: " "$plan_file" 2>/dev/null | \
-        head -1 | \
-        sed "s|^\*\*${field_pattern}\*\*: ||" | \
-        sed 's/^[ \t]*//;s/[ \t]*$//' | \
-        grep -v "NEEDS CLARIFICATION" | \
-        grep -v "^N/A$" || echo ""
-}
-
-parse_plan_data() {
-    local plan_file="$1"
-    
-    if [[ ! -f "$plan_file" ]]; then
-        log_error "Plan file not found: $plan_file"
-        return 1
-    fi
-    
-    if [[ ! -r "$plan_file" ]]; then
-        log_error "Plan file is not readable: $plan_file"
-        return 1
-    fi
-    
-    log_info "Parsing plan data from $plan_file"
-    
-    NEW_LANG=$(extract_plan_field "Language/Version" "$plan_file")
-    NEW_FRAMEWORK=$(extract_plan_field "Primary Dependencies" "$plan_file")
-    NEW_DB=$(extract_plan_field "Storage" "$plan_file")
-    NEW_PROJECT_TYPE=$(extract_plan_field "Project Type" "$plan_file")
-    
-    # Log what we found
-    if [[ -n "$NEW_LANG" ]]; then
-        log_info "Found language: $NEW_LANG"
-    else
-        log_warning "No language information found in plan"
-    fi
-    
-    if [[ -n "$NEW_FRAMEWORK" ]]; then
-        log_info "Found framework: $NEW_FRAMEWORK"
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]]; then
-        log_info "Found database: $NEW_DB"
-    fi
-    
-    if [[ -n "$NEW_PROJECT_TYPE" ]]; then
-        log_info "Found project type: $NEW_PROJECT_TYPE"
-    fi
-}
-
-format_technology_stack() {
-    local lang="$1"
-    local framework="$2"
-    local parts=()
-    
-    # Add non-empty parts
-    [[ -n "$lang" && "$lang" != "NEEDS CLARIFICATION" ]] && parts+=("$lang")
-    [[ -n "$framework" && "$framework" != "NEEDS CLARIFICATION" && "$framework" != "N/A" ]] && parts+=("$framework")
-    
-    # Join with proper formatting
-    if [[ ${#parts[@]} -eq 0 ]]; then
-        echo ""
-    elif [[ ${#parts[@]} -eq 1 ]]; then
-        echo "${parts[0]}"
-    else
-        # Join multiple parts with " + "
-        local result="${parts[0]}"
-        for ((i=1; i<${#parts[@]}; i++)); do
-            result="$result + ${parts[i]}"
-        done
-        echo "$result"
-    fi
-}
-
-#==============================================================================
-# Template and Content Generation Functions
-#==============================================================================
-
-get_project_structure() {
-    local project_type="$1"
-    
-    if [[ "$project_type" == *"web"* ]]; then
-        echo "backend/\\nfrontend/\\ntests/"
-    else
-        echo "src/\\ntests/"
-    fi
-}
-
-get_commands_for_language() {
-    local lang="$1"
-    
-    case "$lang" in
-        *"Python"*)
-            echo "cd src && pytest && ruff check ."
-            ;;
-        *"Rust"*)
-            echo "cargo test && cargo clippy"
-            ;;
-        *"JavaScript"*|*"TypeScript"*)
-            echo "npm test && npm run lint"
-            ;;
-        *)
-            echo "# Add commands for $lang"
-            ;;
-    esac
-}
-
-get_language_conventions() {
-    local lang="$1"
-    echo "$lang: Follow standard conventions"
-}
-
-# Escape sed replacement-side specials for | delimiter.
-# & and \ are replacement-side specials; | is our sed delimiter.
-_esc_sed() { printf '%s\n' "$1" | sed 's/[\\&|]/\\&/g'; }
-
-create_new_agent_file() {
-    local target_file="$1"
-    local temp_file="$2"
-    local project_name
-    project_name=$(_esc_sed "$3")
-    local current_date="$4"
-    
-    if [[ ! -f "$TEMPLATE_FILE" ]]; then
-        log_error "Template not found at $TEMPLATE_FILE"
-        return 1
-    fi
-    
-    if [[ ! -r "$TEMPLATE_FILE" ]]; then
-        log_error "Template file is not readable: $TEMPLATE_FILE"
-        return 1
-    fi
-    
-    log_info "Creating new agent context file from template..."
-    
-    if ! cp "$TEMPLATE_FILE" "$temp_file"; then
-        log_error "Failed to copy template file"
-        return 1
-    fi
-    
-    # Replace template placeholders
-    local project_structure
-    project_structure=$(get_project_structure "$NEW_PROJECT_TYPE")
-    project_structure=$(_esc_sed "$project_structure")
-    
-    local commands
-    commands=$(get_commands_for_language "$NEW_LANG")
-
-    local language_conventions
-    language_conventions=$(get_language_conventions "$NEW_LANG")
-
-    local escaped_lang=$(_esc_sed "$NEW_LANG")
-    local escaped_framework=$(_esc_sed "$NEW_FRAMEWORK")
-    commands=$(_esc_sed "$commands")
-    language_conventions=$(_esc_sed "$language_conventions")
-    local escaped_branch=$(_esc_sed "$CURRENT_BRANCH")
-    
-    # Build technology stack and recent change strings conditionally
-    local tech_stack
-    if [[ -n "$escaped_lang" && -n "$escaped_framework" ]]; then
-        tech_stack="- $escaped_lang + $escaped_framework ($escaped_branch)"
-    elif [[ -n "$escaped_lang" ]]; then
-        tech_stack="- $escaped_lang ($escaped_branch)"
-    elif [[ -n "$escaped_framework" ]]; then
-        tech_stack="- $escaped_framework ($escaped_branch)"
-    else
-        tech_stack="- ($escaped_branch)"
-    fi
-
-    local recent_change
-    if [[ -n "$escaped_lang" && -n "$escaped_framework" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_lang + $escaped_framework"
-    elif [[ -n "$escaped_lang" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_lang"
-    elif [[ -n "$escaped_framework" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_framework"
-    else
-        recent_change="- $escaped_branch: Added"
-    fi
-
-    local substitutions=(
-        "s|\[PROJECT NAME\]|$project_name|"
-        "s|\[DATE\]|$current_date|"
-        "s|\[EXTRACTED FROM ALL PLAN.MD FILES\]|$tech_stack|"
-        "s|\[ACTUAL STRUCTURE FROM PLANS\]|$project_structure|g"
-        "s|\[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES\]|$commands|"
-        "s|\[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE\]|$language_conventions|"
-        "s|\[LAST 3 FEATURES AND WHAT THEY ADDED\]|$recent_change|"
-    )
-    
-    for substitution in "${substitutions[@]}"; do
-        if ! sed -i.bak -e "$substitution" "$temp_file"; then
-            log_error "Failed to perform substitution: $substitution"
-            rm -f "$temp_file" "$temp_file.bak"
-            return 1
-        fi
-    done
-    
-    # Convert literal \n sequences to actual newlines (portable — works on BSD + GNU)
-    awk '{gsub(/\\n/,"\n")}1' "$temp_file" > "$temp_file.tmp"
-    mv "$temp_file.tmp" "$temp_file"
-
-    # Clean up backup files from sed -i.bak
-    rm -f "$temp_file.bak"
-
-    # Prepend Cursor frontmatter for .mdc files so rules are auto-included
-    if [[ "$target_file" == *.mdc ]]; then
-        local frontmatter_file
-        frontmatter_file=$(mktemp) || return 1
-        _CLEANUP_FILES+=("$frontmatter_file")
-        printf '%s\n' "---" "description: Project Development Guidelines" "globs: [\"**/*\"]" "alwaysApply: true" "---" "" > "$frontmatter_file"
-        cat "$temp_file" >> "$frontmatter_file"
-        mv "$frontmatter_file" "$temp_file"
-    fi
-
-    return 0
-}
-
-
-
-
-update_existing_agent_file() {
-    local target_file="$1"
-    local current_date="$2"
-    
-    log_info "Updating existing agent context file..."
-    
-    # Use a single temporary file for atomic update
-    local temp_file
-    temp_file=$(mktemp) || {
-        log_error "Failed to create temporary file"
-        return 1
-    }
-    _CLEANUP_FILES+=("$temp_file")
-    
-    # Process the file in one pass
-    local tech_stack=$(format_technology_stack "$NEW_LANG" "$NEW_FRAMEWORK")
-    local new_tech_entries=()
-    local new_change_entry=""
-    
-    # Prepare new technology entries
-    if [[ -n "$tech_stack" ]] && ! grep -q "$tech_stack" "$target_file"; then
-        new_tech_entries+=("- $tech_stack ($CURRENT_BRANCH)")
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]] && [[ "$NEW_DB" != "NEEDS CLARIFICATION" ]] && ! grep -q "$NEW_DB" "$target_file"; then
-        new_tech_entries+=("- $NEW_DB ($CURRENT_BRANCH)")
-    fi
-    
-    # Prepare new change entry
-    if [[ -n "$tech_stack" ]]; then
-        new_change_entry="- $CURRENT_BRANCH: Added $tech_stack"
-    elif [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]] && [[ "$NEW_DB" != "NEEDS CLARIFICATION" ]]; then
-        new_change_entry="- $CURRENT_BRANCH: Added $NEW_DB"
-    fi
-    
-    # Check if sections exist in the file
-    local has_active_technologies=0
-    local has_recent_changes=0
-    
-    if grep -q "^## Active Technologies" "$target_file" 2>/dev/null; then
-        has_active_technologies=1
-    fi
-    
-    if grep -q "^## Recent Changes" "$target_file" 2>/dev/null; then
-        has_recent_changes=1
-    fi
-    
-    # Process file line by line
-    local in_tech_section=false
-    local in_changes_section=false
-    local tech_entries_added=false
-    local changes_entries_added=false
-    local existing_changes_count=0
-    local file_ended=false
-    
-    while IFS= read -r line || [[ -n "$line" ]]; do
-        # Handle Active Technologies section
-        if [[ "$line" == "## Active Technologies" ]]; then
-            echo "$line" >> "$temp_file"
-            in_tech_section=true
-            continue
-        elif [[ $in_tech_section == true ]] && [[ "$line" =~ ^##[[:space:]] ]]; then
-            # Add new tech entries before closing the section
-            if [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-                printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-                tech_entries_added=true
-            fi
-            echo "$line" >> "$temp_file"
-            in_tech_section=false
-            continue
-        elif [[ $in_tech_section == true ]] && [[ -z "$line" ]]; then
-            # Add new tech entries before empty line in tech section
-            if [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-                printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-                tech_entries_added=true
-            fi
-            echo "$line" >> "$temp_file"
-            continue
-        fi
-        
-        # Handle Recent Changes section
-        if [[ "$line" == "## Recent Changes" ]]; then
-            echo "$line" >> "$temp_file"
-            # Add new change entry right after the heading
-            if [[ -n "$new_change_entry" ]]; then
-                echo "$new_change_entry" >> "$temp_file"
-            fi
-            in_changes_section=true
-            changes_entries_added=true
-            continue
-        elif [[ $in_changes_section == true ]] && [[ "$line" =~ ^##[[:space:]] ]]; then
-            echo "$line" >> "$temp_file"
-            in_changes_section=false
-            continue
-        elif [[ $in_changes_section == true ]] && [[ "$line" == "- "* ]]; then
-            # Keep only first 2 existing changes
-            if [[ $existing_changes_count -lt 2 ]]; then
-                echo "$line" >> "$temp_file"
-                ((existing_changes_count++))
-            fi
-            continue
-        fi
-        
-        # Update timestamp
-        if [[ "$line" =~ (\*\*)?Last\ updated(\*\*)?:.*[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] ]]; then
-            echo "$line" | sed "s/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/$current_date/" >> "$temp_file"
-        else
-            echo "$line" >> "$temp_file"
-        fi
-    done < "$target_file"
-    
-    # Post-loop check: if we're still in the Active Technologies section and haven't added new entries
-    if [[ $in_tech_section == true ]] && [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-        printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-        tech_entries_added=true
-    fi
-    
-    # If sections don't exist, add them at the end of the file
-    if [[ $has_active_technologies -eq 0 ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-        echo "" >> "$temp_file"
-        echo "## Active Technologies" >> "$temp_file"
-        printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-        tech_entries_added=true
-    fi
-    
-    if [[ $has_recent_changes -eq 0 ]] && [[ -n "$new_change_entry" ]]; then
-        echo "" >> "$temp_file"
-        echo "## Recent Changes" >> "$temp_file"
-        echo "$new_change_entry" >> "$temp_file"
-        changes_entries_added=true
-    fi
-    
-    # Ensure Cursor .mdc files have YAML frontmatter for auto-inclusion
-    if [[ "$target_file" == *.mdc ]]; then
-        if ! head -1 "$temp_file" | grep -q '^---'; then
-            local frontmatter_file
-            frontmatter_file=$(mktemp) || { rm -f "$temp_file"; return 1; }
-            _CLEANUP_FILES+=("$frontmatter_file")
-            printf '%s\n' "---" "description: Project Development Guidelines" "globs: [\"**/*\"]" "alwaysApply: true" "---" "" > "$frontmatter_file"
-            cat "$temp_file" >> "$frontmatter_file"
-            mv "$frontmatter_file" "$temp_file"
-        fi
-    fi
-
-    # Move temp file to target atomically
-    if ! mv "$temp_file" "$target_file"; then
-        log_error "Failed to update target file"
-        rm -f "$temp_file"
-        return 1
-    fi
-
-    return 0
-}
-#==============================================================================
-# Main Agent File Update Function
-#==============================================================================
-
-update_agent_file() {
-    local target_file="$1"
-    local agent_name="$2"
-    
-    if [[ -z "$target_file" ]] || [[ -z "$agent_name" ]]; then
-        log_error "update_agent_file requires target_file and agent_name parameters"
-        return 1
-    fi
-    
-    log_info "Updating $agent_name context file: $target_file"
-    
-    local project_name
-    project_name=$(basename "$REPO_ROOT")
-    local current_date
-    current_date=$(date +%Y-%m-%d)
-    
-    # Create directory if it doesn't exist
-    local target_dir
-    target_dir=$(dirname "$target_file")
-    if [[ ! -d "$target_dir" ]]; then
-        if ! mkdir -p "$target_dir"; then
-            log_error "Failed to create directory: $target_dir"
-            return 1
-        fi
-    fi
-    
-    if [[ ! -f "$target_file" ]]; then
-        # Create new file from template
-        local temp_file
-        temp_file=$(mktemp) || {
-            log_error "Failed to create temporary file"
-            return 1
-        }
-        _CLEANUP_FILES+=("$temp_file")
-        
-        if create_new_agent_file "$target_file" "$temp_file" "$project_name" "$current_date"; then
-            if mv "$temp_file" "$target_file"; then
-                log_success "Created new $agent_name context file"
-            else
-                log_error "Failed to move temporary file to $target_file"
-                rm -f "$temp_file"
-                return 1
-            fi
-        else
-            log_error "Failed to create new agent file"
-            rm -f "$temp_file"
-            return 1
-        fi
-    else
-        # Update existing file
-        if [[ ! -r "$target_file" ]]; then
-            log_error "Cannot read existing file: $target_file"
-            return 1
-        fi
-        
-        if [[ ! -w "$target_file" ]]; then
-            log_error "Cannot write to existing file: $target_file"
-            return 1
-        fi
-        
-        if update_existing_agent_file "$target_file" "$current_date"; then
-            log_success "Updated existing $agent_name context file"
-        else
-            log_error "Failed to update existing agent file"
-            return 1
-        fi
-    fi
-    
-    return 0
-}
-
-#==============================================================================
-# Agent Selection and Processing
-#==============================================================================
-
-update_specific_agent() {
-    local agent_type="$1"
-    
-    case "$agent_type" in
-        claude)
-            update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
-            ;;
-        gemini)
-            update_agent_file "$GEMINI_FILE" "Gemini CLI" || return 1
-            ;;
-        copilot)
-            update_agent_file "$COPILOT_FILE" "GitHub Copilot" || return 1
-            ;;
-        cursor-agent)
-            update_agent_file "$CURSOR_FILE" "Cursor IDE" || return 1
-            ;;
-        qwen)
-            update_agent_file "$QWEN_FILE" "Qwen Code" || return 1
-            ;;
-        opencode)
-            update_agent_file "$AGENTS_FILE" "opencode" || return 1
-            ;;
-        codex)
-            update_agent_file "$AGENTS_FILE" "Codex CLI" || return 1
-            ;;
-        windsurf)
-            update_agent_file "$WINDSURF_FILE" "Windsurf" || return 1
-            ;;
-        junie)
-            update_agent_file "$JUNIE_FILE" "Junie" || return 1
-            ;;
-        kilocode)
-            update_agent_file "$KILOCODE_FILE" "Kilo Code" || return 1
-            ;;
-        auggie)
-            update_agent_file "$AUGGIE_FILE" "Auggie CLI" || return 1
-            ;;
-        roo)
-            update_agent_file "$ROO_FILE" "Roo Code" || return 1
-            ;;
-        codebuddy)
-            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI" || return 1
-            ;;
-        qodercli)
-            update_agent_file "$QODER_FILE" "Qoder CLI" || return 1
-            ;;
-        amp)
-            update_agent_file "$AMP_FILE" "Amp" || return 1
-            ;;
-        shai)
-            update_agent_file "$SHAI_FILE" "SHAI" || return 1
-            ;;
-        tabnine)
-            update_agent_file "$TABNINE_FILE" "Tabnine CLI" || return 1
-            ;;
-        kiro-cli)
-            update_agent_file "$KIRO_FILE" "Kiro CLI" || return 1
-            ;;
-        agy)
-            update_agent_file "$AGY_FILE" "Antigravity" || return 1
-            ;;
-        bob)
-            update_agent_file "$BOB_FILE" "IBM Bob" || return 1
-            ;;
-        vibe)
-            update_agent_file "$VIBE_FILE" "Mistral Vibe" || return 1
-            ;;
-        kimi)
-            update_agent_file "$KIMI_FILE" "Kimi Code" || return 1
-            ;;
-        trae)
-            update_agent_file "$TRAE_FILE" "Trae" || return 1
-            ;;
-        pi)
-            update_agent_file "$AGENTS_FILE" "Pi Coding Agent" || return 1
-            ;;
-        iflow)
-            update_agent_file "$IFLOW_FILE" "iFlow CLI" || return 1
-            ;;
-        forge)
-            update_agent_file "$AGENTS_FILE" "Forge" || return 1
-            ;;
-        goose)
-            update_agent_file "$AGENTS_FILE" "Goose" || return 1
-            ;;
-        generic)
-            log_info "Generic agent: no predefined context file. Use the agent-specific update script for your agent."
-            ;;
-        *)
-            log_error "Unknown agent type '$agent_type'"
-            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic"
-            exit 1
-            ;;
-    esac
-}
-
-# Helper: skip non-existent files and files already updated (dedup by
-# realpath so that variables pointing to the same file — e.g. AMP_FILE,
-# KIRO_FILE, BOB_FILE all resolving to AGENTS_FILE — are only written once).
-# Uses a linear array instead of associative array for bash 3.2 compatibility.
-# Note: defined at top level because bash 3.2 does not support true
-# nested/local functions. _updated_paths, _found_agent, and _all_ok are
-# initialised exclusively inside update_all_existing_agents so that
-# sourcing this script has no side effects on the caller's environment.
-
-_update_if_new() {
-    local file="$1" name="$2"
-    [[ -f "$file" ]] || return 0
-    local real_path
-    real_path=$(realpath "$file" 2>/dev/null || echo "$file")
-    local p
-    if [[ ${#_updated_paths[@]} -gt 0 ]]; then
-        for p in "${_updated_paths[@]}"; do
-            [[ "$p" == "$real_path" ]] && return 0
-        done
-    fi
-    # Record the file as seen before attempting the update so that:
-    # (a) aliases pointing to the same path are not retried on failure
-    # (b) _found_agent reflects file existence, not update success
-    _updated_paths+=("$real_path")
-    _found_agent=true
-    update_agent_file "$file" "$name"
-}
-
-update_all_existing_agents() {
-    _found_agent=false
-    _updated_paths=()
-    local _all_ok=true
-
-    _update_if_new "$CLAUDE_FILE" "Claude Code"           || _all_ok=false
-    _update_if_new "$GEMINI_FILE" "Gemini CLI"             || _all_ok=false
-    _update_if_new "$COPILOT_FILE" "GitHub Copilot"        || _all_ok=false
-    _update_if_new "$CURSOR_FILE" "Cursor IDE"             || _all_ok=false
-    _update_if_new "$QWEN_FILE" "Qwen Code"                || _all_ok=false
-    _update_if_new "$AGENTS_FILE" "Codex/opencode/Amp/Kiro/Bob/Pi/Forge/Goose" || _all_ok=false
-    _update_if_new "$WINDSURF_FILE" "Windsurf"             || _all_ok=false
-    _update_if_new "$JUNIE_FILE" "Junie"                || _all_ok=false
-    _update_if_new "$KILOCODE_FILE" "Kilo Code"            || _all_ok=false
-    _update_if_new "$AUGGIE_FILE" "Auggie CLI"             || _all_ok=false
-    _update_if_new "$ROO_FILE" "Roo Code"                  || _all_ok=false
-    _update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"       || _all_ok=false
-    _update_if_new "$SHAI_FILE" "SHAI"                     || _all_ok=false
-    _update_if_new "$TABNINE_FILE" "Tabnine CLI"           || _all_ok=false
-    _update_if_new "$QODER_FILE" "Qoder CLI"               || _all_ok=false
-    _update_if_new "$AGY_FILE" "Antigravity"               || _all_ok=false
-    _update_if_new "$VIBE_FILE" "Mistral Vibe"             || _all_ok=false
-    _update_if_new "$KIMI_FILE" "Kimi Code"                || _all_ok=false
-    _update_if_new "$TRAE_FILE" "Trae"                     || _all_ok=false
-    _update_if_new "$IFLOW_FILE" "iFlow CLI"               || _all_ok=false
-
-    # If no agent files exist, create a default Claude file
-    if [[ "$_found_agent" == false ]]; then
-        log_info "No existing agent files found, creating default Claude file..."
-        update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
-    fi
-
-    [[ "$_all_ok" == true ]]
-}
-print_summary() {
-    echo
-    log_info "Summary of changes:"
-    
-    if [[ -n "$NEW_LANG" ]]; then
-        echo "  - Added language: $NEW_LANG"
-    fi
-    
-    if [[ -n "$NEW_FRAMEWORK" ]]; then
-        echo "  - Added framework: $NEW_FRAMEWORK"
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]]; then
-        echo "  - Added database: $NEW_DB"
-    fi
-    
-    echo
-    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic]"
-}
-
-#==============================================================================
-# Main Execution
-#==============================================================================
-
-main() {
-    # Validate environment before proceeding
-    validate_environment
-    
-    log_info "=== Updating agent context files for feature $CURRENT_BRANCH ==="
-    
-    # Parse the plan file to extract project information
-    if ! parse_plan_data "$NEW_PLAN"; then
-        log_error "Failed to parse plan data"
-        exit 1
-    fi
-    
-    # Process based on agent type argument
-    local success=true
-    
-    if [[ -z "$AGENT_TYPE" ]]; then
-        # No specific agent provided - update all existing agent files
-        log_info "No agent specified, updating all existing agent files..."
-        if ! update_all_existing_agents; then
-            success=false
-        fi
-    else
-        # Specific agent provided - update only that agent
-        log_info "Updating specific agent: $AGENT_TYPE"
-        if ! update_specific_agent "$AGENT_TYPE"; then
-            success=false
-        fi
-    fi
-    
-    # Print summary
-    print_summary
-    
-    if [[ "$success" == true ]]; then
-        log_success "Agent context update completed successfully"
-        exit 0
-    else
-        log_error "Agent context update completed with errors"
-        exit 1
-    fi
-}
-
-# Execute main function if script is run directly
-if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
-    main "$@"
-fi
diff --git a/scripts/powershell/update-agent-context.ps1 b/scripts/powershell/update-agent-context.ps1
deleted file mode 100644
index 3ee45d383c..0000000000
--- a/scripts/powershell/update-agent-context.ps1
+++ /dev/null
@@ -1,515 +0,0 @@
-#!/usr/bin/env pwsh
-<#!
-.SYNOPSIS
-Update agent context files with information from plan.md (PowerShell version)
-
-.DESCRIPTION
-Mirrors the behavior of scripts/bash/update-agent-context.sh:
- 1. Environment Validation
- 2. Plan Data Extraction
- 3. Agent File Management (create from template or update existing)
- 4. Content Generation (technology stack, recent changes, timestamp)
- 5. Multi-Agent Support (claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, junie, kilocode, auggie, roo, codebuddy, amp, shai, tabnine, kiro-cli, agy, bob, vibe, qodercli, kimi, trae, pi, iflow, forge, goose, generic)
-
-.PARAMETER AgentType
-Optional agent key to update a single agent. If omitted, updates all existing agent files (creating a default Claude file if none exist).
-
-.EXAMPLE
-./update-agent-context.ps1 -AgentType claude
-
-.EXAMPLE
-./update-agent-context.ps1   # Updates all existing agent files
-
-.NOTES
-Relies on common helper functions in common.ps1
-#>
-param(
-    [Parameter(Position=0)]
-    [ValidateSet('claude','gemini','copilot','cursor-agent','qwen','opencode','codex','windsurf','junie','kilocode','auggie','roo','codebuddy','amp','shai','tabnine','kiro-cli','agy','bob','vibe','qodercli','kimi','trae','pi','iflow','forge','goose','generic')]
-    [string]$AgentType
-)
-
-$ErrorActionPreference = 'Stop'
-
-# Import common helpers
-$ScriptDir = Split-Path -Parent $MyInvocation.MyCommand.Path
-. (Join-Path $ScriptDir 'common.ps1')
-
-# Acquire environment paths
-$envData = Get-FeaturePathsEnv
-$REPO_ROOT     = $envData.REPO_ROOT
-$CURRENT_BRANCH = $envData.CURRENT_BRANCH
-$HAS_GIT       = $envData.HAS_GIT
-$IMPL_PLAN     = $envData.IMPL_PLAN
-$NEW_PLAN = $IMPL_PLAN
-
-# Agent file paths
-$CLAUDE_FILE   = Join-Path $REPO_ROOT 'CLAUDE.md'
-$GEMINI_FILE   = Join-Path $REPO_ROOT 'GEMINI.md'
-$COPILOT_FILE  = Join-Path $REPO_ROOT '.github/copilot-instructions.md'
-$CURSOR_FILE   = Join-Path $REPO_ROOT '.cursor/rules/specify-rules.mdc'
-$QWEN_FILE     = Join-Path $REPO_ROOT 'QWEN.md'
-$AGENTS_FILE   = Join-Path $REPO_ROOT 'AGENTS.md'
-$WINDSURF_FILE = Join-Path $REPO_ROOT '.windsurf/rules/specify-rules.md'
-$JUNIE_FILE = Join-Path $REPO_ROOT '.junie/AGENTS.md'
-$KILOCODE_FILE = Join-Path $REPO_ROOT '.kilocode/rules/specify-rules.md'
-$AUGGIE_FILE   = Join-Path $REPO_ROOT '.augment/rules/specify-rules.md'
-$ROO_FILE      = Join-Path $REPO_ROOT '.roo/rules/specify-rules.md'
-$CODEBUDDY_FILE = Join-Path $REPO_ROOT 'CODEBUDDY.md'
-$QODER_FILE    = Join-Path $REPO_ROOT 'QODER.md'
-$AMP_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
-$SHAI_FILE     = Join-Path $REPO_ROOT 'SHAI.md'
-$TABNINE_FILE  = Join-Path $REPO_ROOT 'TABNINE.md'
-$KIRO_FILE     = Join-Path $REPO_ROOT 'AGENTS.md'
-$AGY_FILE      = Join-Path $REPO_ROOT '.agent/rules/specify-rules.md'
-$BOB_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
-$VIBE_FILE     = Join-Path $REPO_ROOT '.vibe/agents/specify-agents.md'
-$KIMI_FILE     = Join-Path $REPO_ROOT 'KIMI.md'
-$TRAE_FILE     = Join-Path $REPO_ROOT '.trae/rules/project_rules.md'
-$IFLOW_FILE    = Join-Path $REPO_ROOT 'IFLOW.md'
-$FORGE_FILE    = Join-Path $REPO_ROOT 'AGENTS.md'
-$GOOSE_FILE    = Join-Path $REPO_ROOT 'AGENTS.md'
-
-$TEMPLATE_FILE = Join-Path $REPO_ROOT '.specify/templates/agent-file-template.md'
-
-# Parsed plan data placeholders
-$script:NEW_LANG = ''
-$script:NEW_FRAMEWORK = ''
-$script:NEW_DB = ''
-$script:NEW_PROJECT_TYPE = ''
-
-function Write-Info { 
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Message
-    )
-    Write-Host "INFO: $Message" 
-}
-
-function Write-Success { 
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Message
-    )
-    Write-Host "$([char]0x2713) $Message" 
-}
-
-function Write-WarningMsg { 
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Message
-    )
-    Write-Warning $Message 
-}
-
-function Write-Err { 
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Message
-    )
-    Write-Host "ERROR: $Message" -ForegroundColor Red 
-}
-
-function Validate-Environment {
-    if (-not $CURRENT_BRANCH) {
-        Write-Err 'Unable to determine current feature'
-        if ($HAS_GIT) { Write-Info "Make sure you're on a feature branch" } else { Write-Info 'Set SPECIFY_FEATURE environment variable or create a feature first' }
-        exit 1
-    }
-    if (-not (Test-Path $NEW_PLAN)) {
-        Write-Err "No plan.md found at $NEW_PLAN"
-        Write-Info 'Ensure you are working on a feature with a corresponding spec directory'
-        if (-not $HAS_GIT) { Write-Info 'Use: $env:SPECIFY_FEATURE=your-feature-name or create a new feature first' }
-        exit 1
-    }
-    if (-not (Test-Path $TEMPLATE_FILE)) {
-        Write-Err "Template file not found at $TEMPLATE_FILE"
-        Write-Info 'Run specify init to scaffold .specify/templates, or add agent-file-template.md there.'
-        exit 1
-    }
-}
-
-function Extract-PlanField {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$FieldPattern,
-        [Parameter(Mandatory=$true)]
-        [string]$PlanFile
-    )
-    if (-not (Test-Path $PlanFile)) { return '' }
-    # Lines like **Language/Version**: Python 3.12
-    $regex = "^\*\*$([Regex]::Escape($FieldPattern))\*\*: (.+)$"
-    Get-Content -LiteralPath $PlanFile -Encoding utf8 | ForEach-Object {
-        if ($_ -match $regex) { 
-            $val = $Matches[1].Trim()
-            if ($val -notin @('NEEDS CLARIFICATION','N/A')) { return $val }
-        }
-    } | Select-Object -First 1
-}
-
-function Parse-PlanData {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$PlanFile
-    )
-    if (-not (Test-Path $PlanFile)) { Write-Err "Plan file not found: $PlanFile"; return $false }
-    Write-Info "Parsing plan data from $PlanFile"
-    $script:NEW_LANG        = Extract-PlanField -FieldPattern 'Language/Version' -PlanFile $PlanFile
-    $script:NEW_FRAMEWORK   = Extract-PlanField -FieldPattern 'Primary Dependencies' -PlanFile $PlanFile
-    $script:NEW_DB          = Extract-PlanField -FieldPattern 'Storage' -PlanFile $PlanFile
-    $script:NEW_PROJECT_TYPE = Extract-PlanField -FieldPattern 'Project Type' -PlanFile $PlanFile
-
-    if ($NEW_LANG) { Write-Info "Found language: $NEW_LANG" } else { Write-WarningMsg 'No language information found in plan' }
-    if ($NEW_FRAMEWORK) { Write-Info "Found framework: $NEW_FRAMEWORK" }
-    if ($NEW_DB -and $NEW_DB -ne 'N/A') { Write-Info "Found database: $NEW_DB" }
-    if ($NEW_PROJECT_TYPE) { Write-Info "Found project type: $NEW_PROJECT_TYPE" }
-    return $true
-}
-
-function Format-TechnologyStack {
-    param(
-        [Parameter(Mandatory=$false)]
-        [string]$Lang,
-        [Parameter(Mandatory=$false)]
-        [string]$Framework
-    )
-    $parts = @()
-    if ($Lang -and $Lang -ne 'NEEDS CLARIFICATION') { $parts += $Lang }
-    if ($Framework -and $Framework -notin @('NEEDS CLARIFICATION','N/A')) { $parts += $Framework }
-    if (-not $parts) { return '' }
-    return ($parts -join ' + ')
-}
-
-function Get-ProjectStructure { 
-    param(
-        [Parameter(Mandatory=$false)]
-        [string]$ProjectType
-    )
-    if ($ProjectType -match 'web') { return "backend/`nfrontend/`ntests/" } else { return "src/`ntests/" } 
-}
-
-function Get-CommandsForLanguage { 
-    param(
-        [Parameter(Mandatory=$false)]
-        [string]$Lang
-    )
-    switch -Regex ($Lang) {
-        'Python' { return "cd src; pytest; ruff check ." }
-        'Rust' { return "cargo test; cargo clippy" }
-        'JavaScript|TypeScript' { return "npm test; npm run lint" }
-        default { return "# Add commands for $Lang" }
-    }
-}
-
-function Get-LanguageConventions { 
-    param(
-        [Parameter(Mandatory=$false)]
-        [string]$Lang
-    )
-    if ($Lang) { "${Lang}: Follow standard conventions" } else { 'General: Follow standard conventions' } 
-}
-
-function New-AgentFile {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$TargetFile,
-        [Parameter(Mandatory=$true)]
-        [string]$ProjectName,
-        [Parameter(Mandatory=$true)]
-        [datetime]$Date
-    )
-    if (-not (Test-Path $TEMPLATE_FILE)) { Write-Err "Template not found at $TEMPLATE_FILE"; return $false }
-    $temp = New-TemporaryFile
-    Copy-Item -LiteralPath $TEMPLATE_FILE -Destination $temp -Force
-
-    $projectStructure = Get-ProjectStructure -ProjectType $NEW_PROJECT_TYPE
-    $commands = Get-CommandsForLanguage -Lang $NEW_LANG
-    $languageConventions = Get-LanguageConventions -Lang $NEW_LANG
-
-    $escaped_lang = $NEW_LANG
-    $escaped_framework = $NEW_FRAMEWORK
-    $escaped_branch = $CURRENT_BRANCH
-
-    $content = Get-Content -LiteralPath $temp -Raw -Encoding utf8
-    $content = $content -replace '\[PROJECT NAME\]',$ProjectName
-    $content = $content -replace '\[DATE\]',$Date.ToString('yyyy-MM-dd')
-    
-    # Build the technology stack string safely
-    $techStackForTemplate = ""
-    if ($escaped_lang -and $escaped_framework) {
-        $techStackForTemplate = "- $escaped_lang + $escaped_framework ($escaped_branch)"
-    } elseif ($escaped_lang) {
-        $techStackForTemplate = "- $escaped_lang ($escaped_branch)"
-    } elseif ($escaped_framework) {
-        $techStackForTemplate = "- $escaped_framework ($escaped_branch)"
-    }
-    
-    $content = $content -replace '\[EXTRACTED FROM ALL PLAN.MD FILES\]',$techStackForTemplate
-    # For project structure we manually embed (keep newlines)
-    $escapedStructure = [Regex]::Escape($projectStructure)
-    $content = $content -replace '\[ACTUAL STRUCTURE FROM PLANS\]',$escapedStructure
-    # Replace escaped newlines placeholder after all replacements
-    $content = $content -replace '\[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES\]',$commands
-    $content = $content -replace '\[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE\]',$languageConventions
-    
-    # Build the recent changes string safely
-    $recentChangesForTemplate = ""
-    if ($escaped_lang -and $escaped_framework) {
-        $recentChangesForTemplate = "- ${escaped_branch}: Added ${escaped_lang} + ${escaped_framework}"
-    } elseif ($escaped_lang) {
-        $recentChangesForTemplate = "- ${escaped_branch}: Added ${escaped_lang}"
-    } elseif ($escaped_framework) {
-        $recentChangesForTemplate = "- ${escaped_branch}: Added ${escaped_framework}"
-    }
-    
-    $content = $content -replace '\[LAST 3 FEATURES AND WHAT THEY ADDED\]',$recentChangesForTemplate
-    # Convert literal \n sequences introduced by Escape to real newlines
-    $content = $content -replace '\\n',[Environment]::NewLine
-
-    # Prepend Cursor frontmatter for .mdc files so rules are auto-included
-    if ($TargetFile -match '\.mdc$') {
-        $frontmatter = @('---','description: Project Development Guidelines','globs: ["**/*"]','alwaysApply: true','---','') -join [Environment]::NewLine
-        $content = $frontmatter + $content
-    }
-
-    $parent = Split-Path -Parent $TargetFile
-    if (-not (Test-Path $parent)) { New-Item -ItemType Directory -Path $parent | Out-Null }
-    Set-Content -LiteralPath $TargetFile -Value $content -NoNewline -Encoding utf8
-    Remove-Item $temp -Force
-    return $true
-}
-
-function Update-ExistingAgentFile {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$TargetFile,
-        [Parameter(Mandatory=$true)]
-        [datetime]$Date
-    )
-    if (-not (Test-Path $TargetFile)) { return (New-AgentFile -TargetFile $TargetFile -ProjectName (Split-Path $REPO_ROOT -Leaf) -Date $Date) }
-
-    $techStack = Format-TechnologyStack -Lang $NEW_LANG -Framework $NEW_FRAMEWORK
-    $newTechEntries = @()
-    if ($techStack) {
-        $escapedTechStack = [Regex]::Escape($techStack)
-        if (-not (Select-String -Pattern $escapedTechStack -Path $TargetFile -Quiet)) { 
-            $newTechEntries += "- $techStack ($CURRENT_BRANCH)" 
-        }
-    }
-    if ($NEW_DB -and $NEW_DB -notin @('N/A','NEEDS CLARIFICATION')) {
-        $escapedDB = [Regex]::Escape($NEW_DB)
-        if (-not (Select-String -Pattern $escapedDB -Path $TargetFile -Quiet)) { 
-            $newTechEntries += "- $NEW_DB ($CURRENT_BRANCH)" 
-        }
-    }
-    $newChangeEntry = ''
-    if ($techStack) { $newChangeEntry = "- ${CURRENT_BRANCH}: Added ${techStack}" }
-    elseif ($NEW_DB -and $NEW_DB -notin @('N/A','NEEDS CLARIFICATION')) { $newChangeEntry = "- ${CURRENT_BRANCH}: Added ${NEW_DB}" }
-
-    $lines = Get-Content -LiteralPath $TargetFile -Encoding utf8
-    $output = New-Object System.Collections.Generic.List[string]
-    $inTech = $false; $inChanges = $false; $techAdded = $false; $changeAdded = $false; $existingChanges = 0
-
-    for ($i=0; $i -lt $lines.Count; $i++) {
-        $line = $lines[$i]
-        if ($line -eq '## Active Technologies') {
-            $output.Add($line)
-            $inTech = $true
-            continue
-        }
-        if ($inTech -and $line -match '^##\s') {
-            if (-not $techAdded -and $newTechEntries.Count -gt 0) { $newTechEntries | ForEach-Object { $output.Add($_) }; $techAdded = $true }
-            $output.Add($line); $inTech = $false; continue
-        }
-        if ($inTech -and [string]::IsNullOrWhiteSpace($line)) {
-            if (-not $techAdded -and $newTechEntries.Count -gt 0) { $newTechEntries | ForEach-Object { $output.Add($_) }; $techAdded = $true }
-            $output.Add($line); continue
-        }
-        if ($line -eq '## Recent Changes') {
-            $output.Add($line)
-            if ($newChangeEntry) { $output.Add($newChangeEntry); $changeAdded = $true }
-            $inChanges = $true
-            continue
-        }
-        if ($inChanges -and $line -match '^##\s') { $output.Add($line); $inChanges = $false; continue }
-        if ($inChanges -and $line -match '^- ') {
-            if ($existingChanges -lt 2) { $output.Add($line); $existingChanges++ }
-            continue
-        }
-        if ($line -match '(\*\*)?Last updated(\*\*)?: .*\d{4}-\d{2}-\d{2}') {
-            $output.Add(($line -replace '\d{4}-\d{2}-\d{2}',$Date.ToString('yyyy-MM-dd')))
-            continue
-        }
-        $output.Add($line)
-    }
-
-    # Post-loop check: if we're still in the Active Technologies section and haven't added new entries
-    if ($inTech -and -not $techAdded -and $newTechEntries.Count -gt 0) {
-        $newTechEntries | ForEach-Object { $output.Add($_) }
-    }
-
-    # Ensure Cursor .mdc files have YAML frontmatter for auto-inclusion
-    if ($TargetFile -match '\.mdc$' -and $output.Count -gt 0 -and $output[0] -ne '---') {
-        $frontmatter = @('---','description: Project Development Guidelines','globs: ["**/*"]','alwaysApply: true','---','')
-        $output.InsertRange(0, $frontmatter)
-    }
-
-    Set-Content -LiteralPath $TargetFile -Value ($output -join [Environment]::NewLine) -Encoding utf8
-    return $true
-}
-
-function Update-AgentFile {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$TargetFile,
-        [Parameter(Mandatory=$true)]
-        [string]$AgentName
-    )
-    if (-not $TargetFile -or -not $AgentName) { Write-Err 'Update-AgentFile requires TargetFile and AgentName'; return $false }
-    Write-Info "Updating $AgentName context file: $TargetFile"
-    $projectName = Split-Path $REPO_ROOT -Leaf
-    $date = Get-Date
-
-    $dir = Split-Path -Parent $TargetFile
-    if (-not (Test-Path $dir)) { New-Item -ItemType Directory -Path $dir | Out-Null }
-
-    if (-not (Test-Path $TargetFile)) {
-        if (New-AgentFile -TargetFile $TargetFile -ProjectName $projectName -Date $date) { Write-Success "Created new $AgentName context file" } else { Write-Err 'Failed to create new agent file'; return $false }
-    } else {
-        try {
-            if (Update-ExistingAgentFile -TargetFile $TargetFile -Date $date) { Write-Success "Updated existing $AgentName context file" } else { Write-Err 'Failed to update agent file'; return $false }
-        } catch {
-            Write-Err "Cannot access or update existing file: $TargetFile. $_"
-            return $false
-        }
-    }
-    return $true
-}
-
-function Update-SpecificAgent {
-    param(
-        [Parameter(Mandatory=$true)]
-        [string]$Type
-    )
-    switch ($Type) {
-        'claude'   { Update-AgentFile -TargetFile $CLAUDE_FILE   -AgentName 'Claude Code' }
-        'gemini'   { Update-AgentFile -TargetFile $GEMINI_FILE   -AgentName 'Gemini CLI' }
-        'copilot'  { Update-AgentFile -TargetFile $COPILOT_FILE  -AgentName 'GitHub Copilot' }
-        'cursor-agent' { Update-AgentFile -TargetFile $CURSOR_FILE   -AgentName 'Cursor IDE' }
-        'qwen'     { Update-AgentFile -TargetFile $QWEN_FILE     -AgentName 'Qwen Code' }
-        'opencode' { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'opencode' }
-        'codex'    { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'Codex CLI' }
-        'windsurf' { Update-AgentFile -TargetFile $WINDSURF_FILE -AgentName 'Windsurf' }
-        'junie'    { Update-AgentFile -TargetFile $JUNIE_FILE    -AgentName 'Junie' }
-        'kilocode' { Update-AgentFile -TargetFile $KILOCODE_FILE -AgentName 'Kilo Code' }
-        'auggie'   { Update-AgentFile -TargetFile $AUGGIE_FILE   -AgentName 'Auggie CLI' }
-        'roo'      { Update-AgentFile -TargetFile $ROO_FILE      -AgentName 'Roo Code' }
-        'codebuddy' { Update-AgentFile -TargetFile $CODEBUDDY_FILE -AgentName 'CodeBuddy CLI' }
-        'qodercli' { Update-AgentFile -TargetFile $QODER_FILE    -AgentName 'Qoder CLI' }
-        'amp'      { Update-AgentFile -TargetFile $AMP_FILE      -AgentName 'Amp' }
-        'shai'     { Update-AgentFile -TargetFile $SHAI_FILE     -AgentName 'SHAI' }
-        'tabnine'  { Update-AgentFile -TargetFile $TABNINE_FILE  -AgentName 'Tabnine CLI' }
-        'kiro-cli' { Update-AgentFile -TargetFile $KIRO_FILE     -AgentName 'Kiro CLI' }
-        'agy'      { Update-AgentFile -TargetFile $AGY_FILE      -AgentName 'Antigravity' }
-        'bob'      { Update-AgentFile -TargetFile $BOB_FILE      -AgentName 'IBM Bob' }
-        'vibe'     { Update-AgentFile -TargetFile $VIBE_FILE     -AgentName 'Mistral Vibe' }
-        'kimi'     { Update-AgentFile -TargetFile $KIMI_FILE     -AgentName 'Kimi Code' }
-        'trae'     { Update-AgentFile -TargetFile $TRAE_FILE     -AgentName 'Trae' }
-        'pi'       { Update-AgentFile -TargetFile $AGENTS_FILE   -AgentName 'Pi Coding Agent' }
-        'iflow'    { Update-AgentFile -TargetFile $IFLOW_FILE    -AgentName 'iFlow CLI' }
-        'forge'    { Update-AgentFile -TargetFile $FORGE_FILE    -AgentName 'Forge' }
-        'goose'    { Update-AgentFile -TargetFile $GOOSE_FILE    -AgentName 'Goose' }
-        'generic'  { Write-Info 'Generic agent: no predefined context file. Use the agent-specific update script for your agent.' }
-        default { Write-Err "Unknown agent type '$Type'"; Write-Err 'Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic'; return $false }
-    }
-}
-
-function Update-AllExistingAgents {
-    $found = $false
-    $ok = $true
-    $updatedPaths = @()
-    
-    # Helper function to update only if file exists and hasn't been updated yet
-    function Update-IfNew {
-        param(
-            [Parameter(Mandatory=$true)]
-            [string]$FilePath,
-            [Parameter(Mandatory=$true)]
-            [string]$AgentName
-        )
-        
-        if (-not (Test-Path $FilePath)) { return $true }
-        
-        # Get the real path to detect duplicates (e.g., AMP_FILE, KIRO_FILE, BOB_FILE all point to AGENTS.md)
-        $realPath = (Get-Item -LiteralPath $FilePath).FullName
-        
-        # Check if we've already updated this file
-        if ($updatedPaths -contains $realPath) {
-            return $true
-        }
-        
-        # Record the file as seen before attempting the update
-        # Use parent scope (1) to modify Update-AllExistingAgents' local variables
-        Set-Variable -Name updatedPaths -Value ($updatedPaths + $realPath) -Scope 1
-        Set-Variable -Name found -Value $true -Scope 1
-        
-        # Perform the update
-        return (Update-AgentFile -TargetFile $FilePath -AgentName $AgentName)
-    }
-    
-    if (-not (Update-IfNew -FilePath $CLAUDE_FILE   -AgentName 'Claude Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $GEMINI_FILE   -AgentName 'Gemini CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $COPILOT_FILE  -AgentName 'GitHub Copilot')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $CURSOR_FILE   -AgentName 'Cursor IDE')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $QWEN_FILE     -AgentName 'Qwen Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $AGENTS_FILE   -AgentName 'Codex/opencode/Amp/Kiro/Bob/Pi/Forge/Goose')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $WINDSURF_FILE -AgentName 'Windsurf')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $JUNIE_FILE    -AgentName 'Junie')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $KILOCODE_FILE -AgentName 'Kilo Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $AUGGIE_FILE   -AgentName 'Auggie CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $ROO_FILE      -AgentName 'Roo Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $CODEBUDDY_FILE -AgentName 'CodeBuddy CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $QODER_FILE    -AgentName 'Qoder CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $SHAI_FILE     -AgentName 'SHAI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $TABNINE_FILE  -AgentName 'Tabnine CLI')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $AGY_FILE      -AgentName 'Antigravity')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $VIBE_FILE     -AgentName 'Mistral Vibe')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $KIMI_FILE     -AgentName 'Kimi Code')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $TRAE_FILE     -AgentName 'Trae')) { $ok = $false }
-    if (-not (Update-IfNew -FilePath $IFLOW_FILE    -AgentName 'iFlow CLI')) { $ok = $false }
-    
-    if (-not $found) {
-        Write-Info 'No existing agent files found, creating default Claude file...'
-        if (-not (Update-AgentFile -TargetFile $CLAUDE_FILE -AgentName 'Claude Code')) { $ok = $false }
-    }
-    return $ok
-}
-
-function Print-Summary {
-    Write-Host ''
-    Write-Info 'Summary of changes:'
-    if ($NEW_LANG) { Write-Host "  - Added language: $NEW_LANG" }
-    if ($NEW_FRAMEWORK) { Write-Host "  - Added framework: $NEW_FRAMEWORK" }
-    if ($NEW_DB -and $NEW_DB -ne 'N/A') { Write-Host "  - Added database: $NEW_DB" }
-    Write-Host ''
-    Write-Info 'Usage: ./update-agent-context.ps1 [-AgentType claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|junie|kilocode|auggie|roo|codebuddy|amp|shai|tabnine|kiro-cli|agy|bob|vibe|qodercli|kimi|trae|pi|iflow|forge|goose|generic]'
-}
-
-function Main {
-    Validate-Environment
-    Write-Info "=== Updating agent context files for feature $CURRENT_BRANCH ==="
-    if (-not (Parse-PlanData -PlanFile $NEW_PLAN)) { Write-Err 'Failed to parse plan data'; exit 1 }
-    $success = $true
-    if ($AgentType) {
-        Write-Info "Updating specific agent: $AgentType"
-        if (-not (Update-SpecificAgent -Type $AgentType)) { $success = $false }
-    }
-    else {
-        Write-Info 'No agent specified, updating all existing agent files...'
-        if (-not (Update-AllExistingAgents)) { $success = $false }
-    }
-    Print-Summary
-    if ($success) { Write-Success 'Agent context update completed successfully'; exit 0 } else { Write-Err 'Agent context update completed with errors'; exit 1 }
-}
-
-Main
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 0608e7a8ac..8c6fd02b9f 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1261,15 +1261,11 @@ def init(
             manifest.save()
 
             # Write .specify/integration.json
-            script_ext = "sh" if selected_script == "sh" else "ps1"
             integration_json = project_path / ".specify" / "integration.json"
             integration_json.parent.mkdir(parents=True, exist_ok=True)
             integration_json.write_text(json.dumps({
                 "integration": resolved_integration.key,
                 "version": get_speckit_version(),
-                "scripts": {
-                    "update-context": f".specify/integrations/{resolved_integration.key}/scripts/update-context.{script_ext}",
-                },
             }, indent=2) + "\n", encoding="utf-8")
 
             tracker.complete("integration", resolved_integration.config.get("name", resolved_integration.key))
@@ -1373,6 +1369,7 @@ def init(
                 "ai": selected_ai,
                 "integration": resolved_integration.key,
                 "branch_numbering": branch_numbering or "sequential",
+                "context_file": resolved_integration.context_file,
                 "here": here,
                 "preset": preset,
                 "script": selected_script,
@@ -1737,18 +1734,13 @@ def _read_integration_json(project_root: Path) -> dict[str, Any]:
 def _write_integration_json(
     project_root: Path,
     integration_key: str,
-    script_type: str,
 ) -> None:
     """Write ``.specify/integration.json`` for *integration_key*."""
-    script_ext = "sh" if script_type == "sh" else "ps1"
     dest = project_root / INTEGRATION_JSON
     dest.parent.mkdir(parents=True, exist_ok=True)
     dest.write_text(json.dumps({
         "integration": integration_key,
         "version": get_speckit_version(),
-        "scripts": {
-            "update-context": f".specify/integrations/{integration_key}/scripts/update-context.{script_ext}",
-        },
     }, indent=2) + "\n", encoding="utf-8")
 
 
@@ -1936,7 +1928,7 @@ def integration_install(
             raw_options=integration_options,
         )
         manifest.save()
-        _write_integration_json(project_root, integration.key, selected_script)
+        _write_integration_json(project_root, integration.key)
         _update_init_options_for_integration(project_root, integration, script_type=selected_script)
 
     except Exception as e:
@@ -2013,6 +2005,7 @@ def _update_init_options_for_integration(
     opts = load_init_options(project_root)
     opts["integration"] = integration.key
     opts["ai"] = integration.key
+    opts["context_file"] = integration.context_file
     if script_type:
         opts["script"] = script_type
     if isinstance(integration, SkillsIntegration):
@@ -2064,6 +2057,7 @@ def integration_uninstall(
             opts.pop("integration", None)
             opts.pop("ai", None)
             opts.pop("ai_skills", None)
+            opts.pop("context_file", None)
             save_init_options(project_root, opts)
         raise typer.Exit(0)
 
@@ -2082,6 +2076,10 @@ def integration_uninstall(
 
     removed, skipped = manifest.uninstall(project_root, force=force)
 
+    # Remove managed context section from the agent context file
+    if integration:
+        integration.remove_context_section(project_root)
+
     _remove_integration_json(project_root)
 
     # Update init-options.json to clear the integration
@@ -2090,6 +2088,7 @@ def integration_uninstall(
         opts.pop("integration", None)
         opts.pop("ai", None)
         opts.pop("ai_skills", None)
+        opts.pop("context_file", None)
         save_init_options(project_root, opts)
 
     name = (integration.config or {}).get("name", key) if integration else key
@@ -2156,6 +2155,7 @@ def integration_switch(
                 )
                 raise typer.Exit(1)
             removed, skipped = old_manifest.uninstall(project_root, force=force)
+            current_integration.remove_context_section(project_root)
             if removed:
                 console.print(f"  Removed {len(removed)} file(s)")
             if skipped:
@@ -2186,6 +2186,7 @@ def integration_switch(
         opts.pop("integration", None)
         opts.pop("ai", None)
         opts.pop("ai_skills", None)
+        opts.pop("context_file", None)
         save_init_options(project_root, opts)
 
     # Ensure shared infrastructure is present (safe to run unconditionally;
@@ -2212,7 +2213,7 @@ def integration_switch(
             raw_options=integration_options,
         )
         manifest.save()
-        _write_integration_json(project_root, target_integration.key, selected_script)
+        _write_integration_json(project_root, target_integration.key)
         _update_init_options_for_integration(project_root, target_integration, script_type=selected_script)
 
     except Exception as e:
@@ -2320,7 +2321,7 @@ def integration_upgrade(
             raw_options=integration_options,
         )
         new_manifest.save()
-        _write_integration_json(project_root, key, selected_script)
+        _write_integration_json(project_root, key)
         _update_init_options_for_integration(project_root, integration, script_type=selected_script)
     except Exception as exc:
         # Don't teardown — setup overwrites in-place, so teardown would
diff --git a/src/specify_cli/agents.py b/src/specify_cli/agents.py
index 32fc6cdbf0..1a0e5a8317 100644
--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -110,9 +110,9 @@ def _adjust_script_paths(self, frontmatter: dict) -> dict:
         """Normalize script paths in frontmatter to generated project locations.
 
         Rewrites known repo-relative and top-level script paths under the
-        `scripts` and `agent_scripts` keys (for example `../../scripts/`,
-        `../../templates/`, `../../memory/`, `scripts/`, `templates/`, and
-        `memory/`) to the `.specify/...` paths used in generated projects.
+        ``scripts`` key (for example ``../../scripts/``,
+        ``../../templates/``, ``../../memory/``, ``scripts/``, ``templates/``, and
+        ``memory/``) to the ``.specify/...`` paths used in generated projects.
 
         Args:
             frontmatter: Frontmatter dictionary
@@ -122,11 +122,8 @@ def _adjust_script_paths(self, frontmatter: dict) -> dict:
         """
         frontmatter = deepcopy(frontmatter)
 
-        for script_key in ("scripts", "agent_scripts"):
-            scripts = frontmatter.get(script_key)
-            if not isinstance(scripts, dict):
-                continue
-
+        scripts = frontmatter.get("scripts")
+        if isinstance(scripts, dict):
             for key, script_path in scripts.items():
                 if isinstance(script_path, str):
                     scripts[key] = self.rewrite_project_relative_paths(script_path)
@@ -333,11 +330,8 @@ def resolve_skill_placeholders(
             frontmatter = {}
 
         scripts = frontmatter.get("scripts", {}) or {}
-        agent_scripts = frontmatter.get("agent_scripts", {}) or {}
         if not isinstance(scripts, dict):
             scripts = {}
-        if not isinstance(agent_scripts, dict):
-            agent_scripts = {}
 
         init_opts = load_init_options(project_root)
         if not isinstance(init_opts, dict):
@@ -351,17 +345,14 @@ def resolve_skill_placeholders(
             )
             secondary_variant = "sh" if default_variant == "ps" else "ps"
 
-            if default_variant in scripts or default_variant in agent_scripts:
+            if default_variant in scripts:
                 fallback_order.append(default_variant)
-            if secondary_variant in scripts or secondary_variant in agent_scripts:
+            if secondary_variant in scripts:
                 fallback_order.append(secondary_variant)
 
             for key in scripts:
                 if key not in fallback_order:
                     fallback_order.append(key)
-            for key in agent_scripts:
-                if key not in fallback_order:
-                    fallback_order.append(key)
 
             script_variant = fallback_order[0] if fallback_order else None
 
@@ -370,14 +361,12 @@ def resolve_skill_placeholders(
             script_command = script_command.replace("{ARGS}", "$ARGUMENTS")
             body = body.replace("{SCRIPT}", script_command)
 
-        agent_script_command = (
-            agent_scripts.get(script_variant) if script_variant else None
-        )
-        if agent_script_command:
-            agent_script_command = agent_script_command.replace("{ARGS}", "$ARGUMENTS")
-            body = body.replace("{AGENT_SCRIPT}", agent_script_command)
-
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
+
+        # Resolve __CONTEXT_FILE__ from init-options
+        context_file = init_opts.get("context_file") or ""
+        body = body.replace("__CONTEXT_FILE__", context_file)
+
         return CommandRegistrar.rewrite_project_relative_paths(body)
 
     def _convert_argument_placeholder(
diff --git a/src/specify_cli/integrations/agy/scripts/update-context.ps1 b/src/specify_cli/integrations/agy/scripts/update-context.ps1
deleted file mode 100644
index 9eeb461657..0000000000
--- a/src/specify_cli/integrations/agy/scripts/update-context.ps1
+++ /dev/null
@@ -1,17 +0,0 @@
-# update-context.ps1 — Antigravity (agy) integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-$ErrorActionPreference = 'Stop'
-
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType agy
diff --git a/src/specify_cli/integrations/agy/scripts/update-context.sh b/src/specify_cli/integrations/agy/scripts/update-context.sh
deleted file mode 100755
index d7303f6197..0000000000
--- a/src/specify_cli/integrations/agy/scripts/update-context.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Antigravity (agy) integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-set -euo pipefail
-
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" agy
diff --git a/src/specify_cli/integrations/amp/scripts/update-context.ps1 b/src/specify_cli/integrations/amp/scripts/update-context.ps1
deleted file mode 100644
index c217b99f9a..0000000000
--- a/src/specify_cli/integrations/amp/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Amp integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType amp
diff --git a/src/specify_cli/integrations/amp/scripts/update-context.sh b/src/specify_cli/integrations/amp/scripts/update-context.sh
deleted file mode 100755
index 56cbf6e787..0000000000
--- a/src/specify_cli/integrations/amp/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Amp integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" amp
diff --git a/src/specify_cli/integrations/auggie/scripts/update-context.ps1 b/src/specify_cli/integrations/auggie/scripts/update-context.ps1
deleted file mode 100644
index 49e7e6b5f3..0000000000
--- a/src/specify_cli/integrations/auggie/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Auggie CLI integration: create/update .augment/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType auggie
diff --git a/src/specify_cli/integrations/auggie/scripts/update-context.sh b/src/specify_cli/integrations/auggie/scripts/update-context.sh
deleted file mode 100755
index 4cf80bba2b..0000000000
--- a/src/specify_cli/integrations/auggie/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Auggie CLI integration: create/update .augment/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" auggie
diff --git a/src/specify_cli/integrations/base.py b/src/specify_cli/integrations/base.py
index 2c01e25b0e..4c71b165e5 100644
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -84,6 +84,11 @@ class IntegrationBase(ABC):
     context_file: str | None = None
     """Relative path to the agent context file (e.g. ``CLAUDE.md``)."""
 
+    # -- Markers for managed context section ------------------------------
+
+    CONTEXT_MARKER_START = "<!-- SPECKIT START -->"
+    CONTEXT_MARKER_END = "<!-- SPECKIT END -->"
+
     # -- Public API -------------------------------------------------------
 
     @classmethod
@@ -380,22 +385,235 @@ def install_scripts(
 
         return created
 
+    # -- Agent context file management ------------------------------------
+
+    @staticmethod
+    def _ensure_mdc_frontmatter(content: str) -> str:
+        """Ensure ``.mdc`` content has YAML frontmatter with ``alwaysApply: true``.
+
+        If frontmatter is missing, prepend it.  If frontmatter exists but
+        ``alwaysApply`` is absent or not ``true``, inject/fix it.
+
+        Uses string/regex manipulation to preserve comments and formatting
+        in existing frontmatter.
+        """
+        import re as _re
+
+        leading_ws = len(content) - len(content.lstrip())
+        leading = content[:leading_ws]
+        stripped = content[leading_ws:]
+
+        if not stripped.startswith("---"):
+            return "---\nalwaysApply: true\n---\n\n" + content
+
+        # Match frontmatter block: ---\n...\n---
+        match = _re.match(
+            r"^(---[ \t]*\r?\n)(.*?)(\r?\n---[ \t]*)(\r?\n|$)(.*)",
+            stripped,
+            _re.DOTALL,
+        )
+        if not match:
+            return "---\nalwaysApply: true\n---\n\n" + content
+
+        opening, fm_text, closing, sep, rest = match.groups()
+        newline = "\r\n" if "\r\n" in opening else "\n"
+
+        # Already correct?
+        if _re.search(
+            r"(?m)^[ \t]*alwaysApply[ \t]*:[ \t]*true[ \t]*(?:#.*)?$", fm_text
+        ):
+            return content
+
+        # alwaysApply exists but wrong value — fix in place while preserving
+        # indentation and any trailing inline comment.
+        if _re.search(r"(?m)^[ \t]*alwaysApply[ \t]*:", fm_text):
+            fm_text = _re.sub(
+                r"(?m)^([ \t]*)alwaysApply[ \t]*:.*?([ \t]*(?:#.*)?)$",
+                r"\1alwaysApply: true\2",
+                fm_text,
+                count=1,
+            )
+        elif fm_text.strip():
+            fm_text = fm_text + newline + "alwaysApply: true"
+        else:
+            fm_text = "alwaysApply: true"
+
+        return f"{leading}{opening}{fm_text}{closing}{sep}{rest}"
+
+    @staticmethod
+    def _build_context_section(plan_path: str = "") -> str:
+        """Build the content for the managed section between markers.
+
+        *plan_path* is the project-relative path to the current plan
+        (e.g. ``"specs/<feature>/plan.md"``).  When empty, the section
+        contains only the generic directive without a concrete path.
+        """
+        lines = [
+            "For additional context about technologies to be used, project structure,",
+            "shell commands, and other important information, read the current plan",
+        ]
+        if plan_path:
+            lines.append(f"at {plan_path}")
+        return "\n".join(lines)
+
+    def upsert_context_section(
+        self,
+        project_root: Path,
+        plan_path: str = "",
+    ) -> Path | None:
+        """Create or update the managed section in the agent context file.
+
+        If the context file does not exist it is created with just the
+        managed section.  If it exists, the content between
+        ``<!-- SPECKIT START -->`` and ``<!-- SPECKIT END -->`` markers
+        is replaced (or appended when no markers are found).
+
+        Returns the path to the context file, or ``None`` when
+        ``context_file`` is not set.
+        """
+        if not self.context_file:
+            return None
+
+        ctx_path = project_root / self.context_file
+        section = (
+            f"{self.CONTEXT_MARKER_START}\n"
+            f"{self._build_context_section(plan_path)}\n"
+            f"{self.CONTEXT_MARKER_END}\n"
+        )
+
+        if ctx_path.exists():
+            content = ctx_path.read_text(encoding="utf-8")
+            start_idx = content.find(self.CONTEXT_MARKER_START)
+            end_idx = content.find(
+                self.CONTEXT_MARKER_END,
+                start_idx if start_idx != -1 else 0,
+            )
+
+            if start_idx != -1 and end_idx != -1 and end_idx > start_idx:
+                # Replace existing section (include the end marker + newline)
+                end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
+                # Consume trailing line ending (CRLF or LF)
+                if end_of_marker < len(content) and content[end_of_marker] == "\r":
+                    end_of_marker += 1
+                if end_of_marker < len(content) and content[end_of_marker] == "\n":
+                    end_of_marker += 1
+                new_content = content[:start_idx] + section + content[end_of_marker:]
+            elif start_idx != -1:
+                # Corrupted: start marker without end — replace from start through EOF
+                new_content = content[:start_idx] + section
+            elif end_idx != -1:
+                # Corrupted: end marker without start — replace BOF through end marker
+                end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
+                if end_of_marker < len(content) and content[end_of_marker] == "\r":
+                    end_of_marker += 1
+                if end_of_marker < len(content) and content[end_of_marker] == "\n":
+                    end_of_marker += 1
+                new_content = section + content[end_of_marker:]
+            else:
+                # No markers found — append
+                if content:
+                    if not content.endswith("\n"):
+                        content += "\n"
+                    new_content = content + "\n" + section
+                else:
+                    new_content = section
+
+            # Ensure .mdc files have required YAML frontmatter
+            if ctx_path.suffix == ".mdc":
+                new_content = self._ensure_mdc_frontmatter(new_content)
+        else:
+            ctx_path.parent.mkdir(parents=True, exist_ok=True)
+            # Cursor .mdc files require YAML frontmatter to be loaded
+            if ctx_path.suffix == ".mdc":
+                new_content = self._ensure_mdc_frontmatter(section)
+            else:
+                new_content = section
+
+        normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
+        ctx_path.write_bytes(normalized.encode("utf-8"))
+        return ctx_path
+
+    def remove_context_section(self, project_root: Path) -> bool:
+        """Remove the managed section from the agent context file.
+
+        Returns ``True`` if the section was found and removed.  If the
+        file becomes empty (or whitespace-only) after removal it is
+        deleted.
+        """
+        if not self.context_file:
+            return False
+
+        ctx_path = project_root / self.context_file
+        if not ctx_path.exists():
+            return False
+
+        content = ctx_path.read_text(encoding="utf-8")
+        start_idx = content.find(self.CONTEXT_MARKER_START)
+        end_idx = content.find(
+            self.CONTEXT_MARKER_END,
+            start_idx if start_idx != -1 else 0,
+        )
+
+        # Only remove a complete, well-ordered managed section. If either
+        # marker is missing, leave the file unchanged to avoid deleting
+        # unrelated user-authored content.
+        if start_idx == -1 or end_idx == -1 or end_idx <= start_idx:
+            return False
+
+        removal_start = start_idx
+        removal_end = end_idx + len(self.CONTEXT_MARKER_END)
+
+        # Consume trailing line ending (CRLF or LF)
+        if removal_end < len(content) and content[removal_end] == "\r":
+            removal_end += 1
+        if removal_end < len(content) and content[removal_end] == "\n":
+            removal_end += 1
+
+        # Also strip a blank line before the section if present
+        if removal_start > 0 and content[removal_start - 1] == "\n":
+            if removal_start > 1 and content[removal_start - 2] == "\n":
+                removal_start -= 1
+
+        new_content = content[:removal_start] + content[removal_end:]
+
+        # Normalize line endings before comparisons
+        normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
+
+        # For .mdc files, treat Speckit-generated frontmatter-only content as empty
+        if ctx_path.suffix == ".mdc":
+            import re
+            # Delete the file if only YAML frontmatter remains (no body content)
+            frontmatter_only = re.match(
+                r"^---\n.*?\n---\s*$", normalized, re.DOTALL
+            )
+            if not normalized.strip() or frontmatter_only:
+                ctx_path.unlink()
+                return True
+
+        if not normalized.strip():
+            ctx_path.unlink()
+        else:
+            ctx_path.write_bytes(normalized.encode("utf-8"))
+
+        return True
+
     @staticmethod
     def process_template(
         content: str,
         agent_name: str,
         script_type: str,
         arg_placeholder: str = "$ARGUMENTS",
+        context_file: str = "",
     ) -> str:
         """Process a raw command template into agent-ready content.
 
         Performs the same transformations as the release script:
         1. Extract ``scripts.<script_type>`` value from YAML frontmatter
         2. Replace ``{SCRIPT}`` with the extracted script command
-        3. Extract ``agent_scripts.<script_type>`` and replace ``{AGENT_SCRIPT}``
-        4. Strip ``scripts:`` and ``agent_scripts:`` sections from frontmatter
-        5. Replace ``{ARGS}`` and ``$ARGUMENTS`` with *arg_placeholder*
-        6. Replace ``__AGENT__`` with *agent_name*
+        3. Strip ``scripts:`` section from frontmatter
+        4. Replace ``{ARGS}`` and ``$ARGUMENTS`` with *arg_placeholder*
+        5. Replace ``__AGENT__`` with *agent_name*
+        6. Replace ``__CONTEXT_FILE__`` with *context_file*
         7. Rewrite paths: ``scripts/`` → ``.specify/scripts/`` etc.
         """
         # 1. Extract script command from frontmatter
@@ -421,25 +639,7 @@ def process_template(
         if script_command:
             content = content.replace("{SCRIPT}", script_command)
 
-        # 3. Extract agent_script command
-        agent_script_command = ""
-        in_agent_scripts = False
-        for line in content.splitlines():
-            if line.strip() == "agent_scripts:":
-                in_agent_scripts = True
-                continue
-            if in_agent_scripts and line and not line[0].isspace():
-                in_agent_scripts = False
-            if in_agent_scripts:
-                m = script_pattern.match(line)
-                if m:
-                    agent_script_command = m.group(1).strip()
-                    break
-
-        if agent_script_command:
-            content = content.replace("{AGENT_SCRIPT}", agent_script_command)
-
-        # 4. Strip scripts: and agent_scripts: sections from frontmatter
+        # 3. Strip scripts: section from frontmatter
         lines = content.splitlines(keepends=True)
         output_lines: list[str] = []
         in_frontmatter = False
@@ -457,23 +657,26 @@ def process_template(
                 output_lines.append(line)
                 continue
             if in_frontmatter:
-                if stripped in ("scripts:", "agent_scripts:"):
+                if stripped == "scripts:":
                     skip_section = True
                     continue
                 if skip_section:
                     if line[0:1].isspace():
-                        continue  # skip indented content under scripts/agent_scripts
+                        continue  # skip indented content under scripts
                     skip_section = False
             output_lines.append(line)
         content = "".join(output_lines)
 
-        # 5. Replace {ARGS} and $ARGUMENTS
+        # 4. Replace {ARGS} and $ARGUMENTS
         content = content.replace("{ARGS}", arg_placeholder)
         content = content.replace("$ARGUMENTS", arg_placeholder)
 
-        # 6. Replace __AGENT__
+        # 5. Replace __AGENT__
         content = content.replace("__AGENT__", agent_name)
 
+        # 6. Replace __CONTEXT_FILE__
+        content = content.replace("__CONTEXT_FILE__", context_file)
+
         # 7. Rewrite paths — delegate to the shared implementation in
         #    CommandRegistrar so extension-local paths are preserved and
         #    boundary rules stay consistent across the codebase.
@@ -526,6 +729,9 @@ def setup(
             self.record_file_in_manifest(dst_file, project_root, manifest)
             created.append(dst_file)
 
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
 
     def teardown(
@@ -539,9 +745,11 @@ def teardown(
 
         Delegates to ``manifest.uninstall()`` which only removes files
         whose hash still matches the recorded value (unless *force*).
+        Also removes the managed context section from the agent file.
 
         Returns ``(removed, skipped)`` file lists.
         """
+        self.remove_context_section(project_root)
         return manifest.uninstall(project_root, force=force)
 
     # -- Convenience helpers for subclasses -------------------------------
@@ -579,8 +787,8 @@ class MarkdownIntegration(IntegrationBase):
     (and optionally ``context_file``).  Everything else is inherited.
 
     ``setup()`` processes command templates (replacing ``{SCRIPT}``,
-    ``{ARGS}``, ``__AGENT__``, rewriting paths) and installs
-    integration-specific scripts (``update-context.sh`` / ``.ps1``).
+    ``{ARGS}``, ``__AGENT__``, rewriting paths) and upserts the
+    managed context section into the agent context file.
     """
 
     def build_exec_args(
@@ -638,7 +846,8 @@ def setup(
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             processed = self.process_template(
-                raw, self.key, script_type, arg_placeholder
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
             )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
@@ -646,7 +855,9 @@ def setup(
             )
             created.append(dst_file)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
 
 
@@ -841,7 +1052,8 @@ def setup(
             raw = src_file.read_text(encoding="utf-8")
             description = self._extract_description(raw)
             processed = self.process_template(
-                raw, self.key, script_type, arg_placeholder
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
             )
             _, body = self._split_frontmatter(processed)
             toml_content = self._render_toml(description, body)
@@ -851,7 +1063,9 @@ def setup(
             )
             created.append(dst_file)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
 
 
@@ -1021,7 +1235,8 @@ def setup(
                 title = self._human_title(src_file.stem)
 
             processed = self.process_template(
-                raw, self.key, script_type, arg_placeholder
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
             )
             _, body = self._split_frontmatter(processed)
             yaml_content = self._render_yaml(
@@ -1033,7 +1248,9 @@ def setup(
             )
             created.append(dst_file)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
 
 
@@ -1176,7 +1393,8 @@ def setup(
 
             # Process body through the standard template pipeline
             processed_body = self.process_template(
-                raw, self.key, script_type, arg_placeholder
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
             )
             # Strip the processed frontmatter — we rebuild it for skills.
             # Preserve leading whitespace in the body to match release ZIP
@@ -1220,5 +1438,7 @@ def _quote(v: str) -> str:
             )
             created.append(dst)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
diff --git a/src/specify_cli/integrations/bob/scripts/update-context.ps1 b/src/specify_cli/integrations/bob/scripts/update-context.ps1
deleted file mode 100644
index 188860899f..0000000000
--- a/src/specify_cli/integrations/bob/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — IBM Bob integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType bob
diff --git a/src/specify_cli/integrations/bob/scripts/update-context.sh b/src/specify_cli/integrations/bob/scripts/update-context.sh
deleted file mode 100755
index 0228603fea..0000000000
--- a/src/specify_cli/integrations/bob/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — IBM Bob integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" bob
diff --git a/src/specify_cli/integrations/claude/scripts/update-context.ps1 b/src/specify_cli/integrations/claude/scripts/update-context.ps1
deleted file mode 100644
index 837974d47a..0000000000
--- a/src/specify_cli/integrations/claude/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Claude Code integration: create/update CLAUDE.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType claude
diff --git a/src/specify_cli/integrations/claude/scripts/update-context.sh b/src/specify_cli/integrations/claude/scripts/update-context.sh
deleted file mode 100755
index 4b83855a27..0000000000
--- a/src/specify_cli/integrations/claude/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Claude Code integration: create/update CLAUDE.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" claude
diff --git a/src/specify_cli/integrations/codebuddy/scripts/update-context.ps1 b/src/specify_cli/integrations/codebuddy/scripts/update-context.ps1
deleted file mode 100644
index 0269392c09..0000000000
--- a/src/specify_cli/integrations/codebuddy/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — CodeBuddy integration: create/update CODEBUDDY.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType codebuddy
diff --git a/src/specify_cli/integrations/codebuddy/scripts/update-context.sh b/src/specify_cli/integrations/codebuddy/scripts/update-context.sh
deleted file mode 100755
index d57ddc3560..0000000000
--- a/src/specify_cli/integrations/codebuddy/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — CodeBuddy integration: create/update CODEBUDDY.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" codebuddy
diff --git a/src/specify_cli/integrations/codex/scripts/update-context.ps1 b/src/specify_cli/integrations/codex/scripts/update-context.ps1
deleted file mode 100644
index d73a5a4d34..0000000000
--- a/src/specify_cli/integrations/codex/scripts/update-context.ps1
+++ /dev/null
@@ -1,17 +0,0 @@
-# update-context.ps1 — Codex CLI integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-$ErrorActionPreference = 'Stop'
-
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType codex
diff --git a/src/specify_cli/integrations/codex/scripts/update-context.sh b/src/specify_cli/integrations/codex/scripts/update-context.sh
deleted file mode 100755
index 512d6e91d3..0000000000
--- a/src/specify_cli/integrations/codex/scripts/update-context.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Codex CLI integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-set -euo pipefail
-
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" codex
diff --git a/src/specify_cli/integrations/copilot/__init__.py b/src/specify_cli/integrations/copilot/__init__.py
index e389138a84..be7fc819f6 100644
--- a/src/specify_cli/integrations/copilot/__init__.py
+++ b/src/specify_cli/integrations/copilot/__init__.py
@@ -183,7 +183,10 @@ def setup(
         # 1. Process and write command files as .agent.md
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
-            processed = self.process_template(raw, self.key, script_type, arg_placeholder)
+            processed = self.process_template(
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
+            )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
                 processed, dest / dst_name, project_root, manifest
@@ -217,8 +220,8 @@ def setup(
                 self.record_file_in_manifest(dst_settings, project_root, manifest)
                 created.append(dst_settings)
 
-        # 4. Install integration-specific update-context scripts
-        created.extend(self.install_scripts(project_root, manifest))
+        # 4. Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
 
         return created
 
diff --git a/src/specify_cli/integrations/copilot/scripts/update-context.ps1 b/src/specify_cli/integrations/copilot/scripts/update-context.ps1
deleted file mode 100644
index 26e746a789..0000000000
--- a/src/specify_cli/integrations/copilot/scripts/update-context.ps1
+++ /dev/null
@@ -1,32 +0,0 @@
-# update-context.ps1 — Copilot integration: create/update .github/copilot-instructions.md
-#
-# This is the copilot-specific implementation that produces the GitHub
-# Copilot instructions file. The shared dispatcher reads
-# .specify/integration.json and calls this script.
-#
-# NOTE: This script is not yet active. It will be activated in Stage 7
-# when the shared update-agent-context.ps1 replaces its switch statement
-# with integration.json-based dispatch. The shared script must also be
-# refactored to support SPECKIT_SOURCE_ONLY (guard the Main call) before
-# dot-sourcing will work.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-# Invoke shared update-agent-context script as a separate process.
-# Dot-sourcing is unsafe until that script guards its Main call.
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType copilot
diff --git a/src/specify_cli/integrations/copilot/scripts/update-context.sh b/src/specify_cli/integrations/copilot/scripts/update-context.sh
deleted file mode 100644
index c7f3bc60b5..0000000000
--- a/src/specify_cli/integrations/copilot/scripts/update-context.sh
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Copilot integration: create/update .github/copilot-instructions.md
-#
-# This is the copilot-specific implementation that produces the GitHub
-# Copilot instructions file. The shared dispatcher reads
-# .specify/integration.json and calls this script.
-#
-# NOTE: This script is not yet active. It will be activated in Stage 7
-# when the shared update-agent-context.sh replaces its case statement
-# with integration.json-based dispatch. The shared script must also be
-# refactored to support SPECKIT_SOURCE_ONLY (guard the main logic)
-# before sourcing will work.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-# Invoke shared update-agent-context script as a separate process.
-# Sourcing is unsafe until that script guards its main logic.
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" copilot
diff --git a/src/specify_cli/integrations/cursor_agent/scripts/update-context.ps1 b/src/specify_cli/integrations/cursor_agent/scripts/update-context.ps1
deleted file mode 100644
index 4ce50a4873..0000000000
--- a/src/specify_cli/integrations/cursor_agent/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Cursor integration: create/update .cursor/rules/specify-rules.mdc
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType cursor-agent
diff --git a/src/specify_cli/integrations/cursor_agent/scripts/update-context.sh b/src/specify_cli/integrations/cursor_agent/scripts/update-context.sh
deleted file mode 100755
index 597ca2289c..0000000000
--- a/src/specify_cli/integrations/cursor_agent/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Cursor integration: create/update .cursor/rules/specify-rules.mdc
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" cursor-agent
diff --git a/src/specify_cli/integrations/forge/__init__.py b/src/specify_cli/integrations/forge/__init__.py
index e1c4d9da62..a941d4c331 100644
--- a/src/specify_cli/integrations/forge/__init__.py
+++ b/src/specify_cli/integrations/forge/__init__.py
@@ -130,7 +130,10 @@ def setup(
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             # Process template with standard MarkdownIntegration logic
-            processed = self.process_template(raw, self.key, script_type, arg_placeholder)
+            processed = self.process_template(
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
+            )
 
             # FORGE-SPECIFIC: Ensure any remaining $ARGUMENTS placeholders are
             # converted to {{parameters}}
@@ -145,8 +148,8 @@ def setup(
             )
             created.append(dst_file)
 
-        # Install integration-specific update-context scripts
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
 
         return created
 
diff --git a/src/specify_cli/integrations/forge/scripts/update-context.ps1 b/src/specify_cli/integrations/forge/scripts/update-context.ps1
deleted file mode 100644
index 474a9c6d0b..0000000000
--- a/src/specify_cli/integrations/forge/scripts/update-context.ps1
+++ /dev/null
@@ -1,33 +0,0 @@
-# update-context.ps1 — Forge integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-$sharedScript = "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1"
-
-# Always delegate to the shared updater; fail clearly if it is unavailable.
-if (-not (Test-Path $sharedScript)) {
-    Write-Error "Error: shared agent context updater not found: $sharedScript"
-    Write-Error "Forge integration requires support in scripts/powershell/update-agent-context.ps1."
-    exit 1
-}
-
-& $sharedScript -AgentType forge
-exit $LASTEXITCODE
diff --git a/src/specify_cli/integrations/forge/scripts/update-context.sh b/src/specify_cli/integrations/forge/scripts/update-context.sh
deleted file mode 100755
index 2a5c46e1d1..0000000000
--- a/src/specify_cli/integrations/forge/scripts/update-context.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Forge integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-shared_script="$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh"
-
-# Always delegate to the shared updater; fail clearly if it is unavailable.
-if [ ! -x "$shared_script" ]; then
-  echo "Error: shared agent context updater not found or not executable:" >&2
-  echo "  $shared_script" >&2
-  echo "Forge integration requires support in scripts/bash/update-agent-context.sh." >&2
-  exit 1
-fi
-
-exec "$shared_script" forge
diff --git a/src/specify_cli/integrations/gemini/scripts/update-context.ps1 b/src/specify_cli/integrations/gemini/scripts/update-context.ps1
deleted file mode 100644
index 51c9e0bc83..0000000000
--- a/src/specify_cli/integrations/gemini/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Gemini CLI integration: create/update GEMINI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType gemini
diff --git a/src/specify_cli/integrations/gemini/scripts/update-context.sh b/src/specify_cli/integrations/gemini/scripts/update-context.sh
deleted file mode 100644
index c4e5003a55..0000000000
--- a/src/specify_cli/integrations/gemini/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Gemini CLI integration: create/update GEMINI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" gemini
diff --git a/src/specify_cli/integrations/generic/__init__.py b/src/specify_cli/integrations/generic/__init__.py
index 4107c48690..fdaee4ed04 100644
--- a/src/specify_cli/integrations/generic/__init__.py
+++ b/src/specify_cli/integrations/generic/__init__.py
@@ -31,7 +31,7 @@ class GenericIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = None
+    context_file = "AGENTS.md"
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:
@@ -122,12 +122,17 @@ def setup(
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
-            processed = self.process_template(raw, self.key, script_type, arg_placeholder)
+            processed = self.process_template(
+                raw, self.key, script_type, arg_placeholder,
+                context_file=self.context_file or "",
+            )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
                 processed, dest / dst_name, project_root, manifest
             )
             created.append(dst_file)
 
-        created.extend(self.install_scripts(project_root, manifest))
+        # Upsert managed context section into the agent context file
+        self.upsert_context_section(project_root)
+
         return created
diff --git a/src/specify_cli/integrations/generic/scripts/update-context.ps1 b/src/specify_cli/integrations/generic/scripts/update-context.ps1
deleted file mode 100644
index 2e9467f801..0000000000
--- a/src/specify_cli/integrations/generic/scripts/update-context.ps1
+++ /dev/null
@@ -1,17 +0,0 @@
-# update-context.ps1 — Generic integration: create/update context file
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-$ErrorActionPreference = 'Stop'
-
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType generic
diff --git a/src/specify_cli/integrations/generic/scripts/update-context.sh b/src/specify_cli/integrations/generic/scripts/update-context.sh
deleted file mode 100755
index d8ad30a7b8..0000000000
--- a/src/specify_cli/integrations/generic/scripts/update-context.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Generic integration: create/update context file
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-set -euo pipefail
-
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" generic
diff --git a/src/specify_cli/integrations/goose/scripts/update-context.ps1 b/src/specify_cli/integrations/goose/scripts/update-context.ps1
deleted file mode 100644
index eeb31f6296..0000000000
--- a/src/specify_cli/integrations/goose/scripts/update-context.ps1
+++ /dev/null
@@ -1,33 +0,0 @@
-# update-context.ps1 — Goose integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-$sharedScript = "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1"
-
-# Always delegate to the shared updater; fail clearly if it is unavailable.
-if (-not (Test-Path $sharedScript)) {
-    Write-Error "Error: shared agent context updater not found: $sharedScript"
-    Write-Error "Goose integration requires support in scripts/powershell/update-agent-context.ps1."
-    exit 1
-}
-
-& $sharedScript -AgentType goose
-exit $LASTEXITCODE
diff --git a/src/specify_cli/integrations/goose/scripts/update-context.sh b/src/specify_cli/integrations/goose/scripts/update-context.sh
deleted file mode 100755
index 759ae3045a..0000000000
--- a/src/specify_cli/integrations/goose/scripts/update-context.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Goose integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-shared_script="$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh"
-
-# Always delegate to the shared updater; fail clearly if it is unavailable.
-if [ ! -x "$shared_script" ]; then
-  echo "Error: shared agent context updater not found or not executable:" >&2
-  echo "  $shared_script" >&2
-  echo "Goose integration requires support in scripts/bash/update-agent-context.sh." >&2
-  exit 1
-fi
-
-exec "$shared_script" goose
diff --git a/src/specify_cli/integrations/iflow/scripts/update-context.ps1 b/src/specify_cli/integrations/iflow/scripts/update-context.ps1
deleted file mode 100644
index b502d4182a..0000000000
--- a/src/specify_cli/integrations/iflow/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — iFlow CLI integration: create/update IFLOW.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType iflow
diff --git a/src/specify_cli/integrations/iflow/scripts/update-context.sh b/src/specify_cli/integrations/iflow/scripts/update-context.sh
deleted file mode 100755
index 5080402071..0000000000
--- a/src/specify_cli/integrations/iflow/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — iFlow CLI integration: create/update IFLOW.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" iflow
diff --git a/src/specify_cli/integrations/junie/scripts/update-context.ps1 b/src/specify_cli/integrations/junie/scripts/update-context.ps1
deleted file mode 100644
index 5a32432132..0000000000
--- a/src/specify_cli/integrations/junie/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Junie integration: create/update .junie/AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType junie
diff --git a/src/specify_cli/integrations/junie/scripts/update-context.sh b/src/specify_cli/integrations/junie/scripts/update-context.sh
deleted file mode 100755
index f4c8ba6c0e..0000000000
--- a/src/specify_cli/integrations/junie/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Junie integration: create/update .junie/AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" junie
diff --git a/src/specify_cli/integrations/kilocode/scripts/update-context.ps1 b/src/specify_cli/integrations/kilocode/scripts/update-context.ps1
deleted file mode 100644
index d87e7ef59f..0000000000
--- a/src/specify_cli/integrations/kilocode/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Kilo Code integration: create/update .kilocode/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType kilocode
diff --git a/src/specify_cli/integrations/kilocode/scripts/update-context.sh b/src/specify_cli/integrations/kilocode/scripts/update-context.sh
deleted file mode 100755
index 132c0403f3..0000000000
--- a/src/specify_cli/integrations/kilocode/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Kilo Code integration: create/update .kilocode/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" kilocode
diff --git a/src/specify_cli/integrations/kimi/scripts/update-context.ps1 b/src/specify_cli/integrations/kimi/scripts/update-context.ps1
deleted file mode 100644
index aa6678d052..0000000000
--- a/src/specify_cli/integrations/kimi/scripts/update-context.ps1
+++ /dev/null
@@ -1,17 +0,0 @@
-# update-context.ps1 — Kimi Code integration: create/update KIMI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-$ErrorActionPreference = 'Stop'
-
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType kimi
diff --git a/src/specify_cli/integrations/kimi/scripts/update-context.sh b/src/specify_cli/integrations/kimi/scripts/update-context.sh
deleted file mode 100755
index 2f81bc2a48..0000000000
--- a/src/specify_cli/integrations/kimi/scripts/update-context.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Kimi Code integration: create/update KIMI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-
-set -euo pipefail
-
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" kimi
diff --git a/src/specify_cli/integrations/kiro_cli/scripts/update-context.ps1 b/src/specify_cli/integrations/kiro_cli/scripts/update-context.ps1
deleted file mode 100644
index 7dd2b35fb7..0000000000
--- a/src/specify_cli/integrations/kiro_cli/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Kiro CLI integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType kiro-cli
diff --git a/src/specify_cli/integrations/kiro_cli/scripts/update-context.sh b/src/specify_cli/integrations/kiro_cli/scripts/update-context.sh
deleted file mode 100755
index fa258edc75..0000000000
--- a/src/specify_cli/integrations/kiro_cli/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Kiro CLI integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" kiro-cli
diff --git a/src/specify_cli/integrations/opencode/scripts/update-context.ps1 b/src/specify_cli/integrations/opencode/scripts/update-context.ps1
deleted file mode 100644
index 4bba02b455..0000000000
--- a/src/specify_cli/integrations/opencode/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — opencode integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType opencode
diff --git a/src/specify_cli/integrations/opencode/scripts/update-context.sh b/src/specify_cli/integrations/opencode/scripts/update-context.sh
deleted file mode 100755
index 24c7e60251..0000000000
--- a/src/specify_cli/integrations/opencode/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — opencode integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" opencode
diff --git a/src/specify_cli/integrations/pi/scripts/update-context.ps1 b/src/specify_cli/integrations/pi/scripts/update-context.ps1
deleted file mode 100644
index 6362118a5b..0000000000
--- a/src/specify_cli/integrations/pi/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Pi Coding Agent integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType pi
diff --git a/src/specify_cli/integrations/pi/scripts/update-context.sh b/src/specify_cli/integrations/pi/scripts/update-context.sh
deleted file mode 100755
index 1ad84c95a2..0000000000
--- a/src/specify_cli/integrations/pi/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Pi Coding Agent integration: create/update AGENTS.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" pi
diff --git a/src/specify_cli/integrations/qodercli/scripts/update-context.ps1 b/src/specify_cli/integrations/qodercli/scripts/update-context.ps1
deleted file mode 100644
index 1fa007a168..0000000000
--- a/src/specify_cli/integrations/qodercli/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Qoder CLI integration: create/update QODER.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType qodercli
diff --git a/src/specify_cli/integrations/qodercli/scripts/update-context.sh b/src/specify_cli/integrations/qodercli/scripts/update-context.sh
deleted file mode 100755
index d371ad7952..0000000000
--- a/src/specify_cli/integrations/qodercli/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Qoder CLI integration: create/update QODER.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" qodercli
diff --git a/src/specify_cli/integrations/qwen/scripts/update-context.ps1 b/src/specify_cli/integrations/qwen/scripts/update-context.ps1
deleted file mode 100644
index 24e4c90fab..0000000000
--- a/src/specify_cli/integrations/qwen/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Qwen Code integration: create/update QWEN.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType qwen
diff --git a/src/specify_cli/integrations/qwen/scripts/update-context.sh b/src/specify_cli/integrations/qwen/scripts/update-context.sh
deleted file mode 100755
index d1c62eb161..0000000000
--- a/src/specify_cli/integrations/qwen/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Qwen Code integration: create/update QWEN.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" qwen
diff --git a/src/specify_cli/integrations/roo/scripts/update-context.ps1 b/src/specify_cli/integrations/roo/scripts/update-context.ps1
deleted file mode 100644
index d1dec923ed..0000000000
--- a/src/specify_cli/integrations/roo/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Roo Code integration: create/update .roo/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType roo
diff --git a/src/specify_cli/integrations/roo/scripts/update-context.sh b/src/specify_cli/integrations/roo/scripts/update-context.sh
deleted file mode 100755
index 8fe255cb1b..0000000000
--- a/src/specify_cli/integrations/roo/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Roo Code integration: create/update .roo/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" roo
diff --git a/src/specify_cli/integrations/shai/scripts/update-context.ps1 b/src/specify_cli/integrations/shai/scripts/update-context.ps1
deleted file mode 100644
index 2c621c76ac..0000000000
--- a/src/specify_cli/integrations/shai/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — SHAI integration: create/update SHAI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType shai
diff --git a/src/specify_cli/integrations/shai/scripts/update-context.sh b/src/specify_cli/integrations/shai/scripts/update-context.sh
deleted file mode 100755
index 093b9d1f76..0000000000
--- a/src/specify_cli/integrations/shai/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — SHAI integration: create/update SHAI.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" shai
diff --git a/src/specify_cli/integrations/tabnine/scripts/update-context.ps1 b/src/specify_cli/integrations/tabnine/scripts/update-context.ps1
deleted file mode 100644
index 0ffb3a1649..0000000000
--- a/src/specify_cli/integrations/tabnine/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Tabnine CLI integration: create/update TABNINE.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType tabnine
diff --git a/src/specify_cli/integrations/tabnine/scripts/update-context.sh b/src/specify_cli/integrations/tabnine/scripts/update-context.sh
deleted file mode 100644
index fe5050b6e9..0000000000
--- a/src/specify_cli/integrations/tabnine/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Tabnine CLI integration: create/update TABNINE.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" tabnine
diff --git a/src/specify_cli/integrations/trae/scripts/update-context.ps1 b/src/specify_cli/integrations/trae/scripts/update-context.ps1
deleted file mode 100644
index ae9a3d1cd0..0000000000
--- a/src/specify_cli/integrations/trae/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Trae integration: create/update .trae/rules/project_rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType trae
diff --git a/src/specify_cli/integrations/trae/scripts/update-context.sh b/src/specify_cli/integrations/trae/scripts/update-context.sh
deleted file mode 100755
index 32e5c16b29..0000000000
--- a/src/specify_cli/integrations/trae/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Trae integration: create/update .trae/rules/project_rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" trae
diff --git a/src/specify_cli/integrations/vibe/scripts/update-context.ps1 b/src/specify_cli/integrations/vibe/scripts/update-context.ps1
deleted file mode 100644
index d82ce3389c..0000000000
--- a/src/specify_cli/integrations/vibe/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Mistral Vibe integration: create/update .vibe/agents/specify-agents.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType vibe
diff --git a/src/specify_cli/integrations/vibe/scripts/update-context.sh b/src/specify_cli/integrations/vibe/scripts/update-context.sh
deleted file mode 100755
index f924cdb896..0000000000
--- a/src/specify_cli/integrations/vibe/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Mistral Vibe integration: create/update .vibe/agents/specify-agents.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" vibe
diff --git a/src/specify_cli/integrations/windsurf/scripts/update-context.ps1 b/src/specify_cli/integrations/windsurf/scripts/update-context.ps1
deleted file mode 100644
index b5fe1d0c0a..0000000000
--- a/src/specify_cli/integrations/windsurf/scripts/update-context.ps1
+++ /dev/null
@@ -1,23 +0,0 @@
-# update-context.ps1 — Windsurf integration: create/update .windsurf/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-$ErrorActionPreference = 'Stop'
-
-# Derive repo root from script location (walks up to find .specify/)
-$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$repoRoot = try { git rev-parse --show-toplevel 2>$null } catch { $null }
-# If git did not return a repo root, or the git root does not contain .specify,
-# fall back to walking up from the script directory to find the initialized project root.
-if (-not $repoRoot -or -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-    $repoRoot = $scriptDir
-    $fsRoot = [System.IO.Path]::GetPathRoot($repoRoot)
-    while ($repoRoot -and $repoRoot -ne $fsRoot -and -not (Test-Path (Join-Path $repoRoot '.specify'))) {
-        $repoRoot = Split-Path -Parent $repoRoot
-    }
-}
-
-& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType windsurf
diff --git a/src/specify_cli/integrations/windsurf/scripts/update-context.sh b/src/specify_cli/integrations/windsurf/scripts/update-context.sh
deleted file mode 100755
index b9a78d320e..0000000000
--- a/src/specify_cli/integrations/windsurf/scripts/update-context.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env bash
-# update-context.sh — Windsurf integration: create/update .windsurf/rules/specify-rules.md
-#
-# Thin wrapper that delegates to the shared update-agent-context script.
-# Activated in Stage 7 when the shared script uses integration.json dispatch.
-#
-# Until then, this delegates to the shared script as a subprocess.
-
-set -euo pipefail
-
-# Derive repo root from script location (walks up to find .specify/)
-_script_dir="$(cd "$(dirname "$0")" && pwd)"
-_root="$_script_dir"
-while [ "$_root" != "/" ] && [ ! -d "$_root/.specify" ]; do _root="$(dirname "$_root")"; done
-if [ -z "${REPO_ROOT:-}" ]; then
-  if [ -d "$_root/.specify" ]; then
-    REPO_ROOT="$_root"
-  else
-    git_root="$(git rev-parse --show-toplevel 2>/dev/null || true)"
-    if [ -n "$git_root" ] && [ -d "$git_root/.specify" ]; then
-      REPO_ROOT="$git_root"
-    else
-      REPO_ROOT="$_root"
-    fi
-  fi
-fi
-
-exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" windsurf
diff --git a/templates/agent-file-template.md b/templates/agent-file-template.md
deleted file mode 100644
index 4cc7fd6678..0000000000
--- a/templates/agent-file-template.md
+++ /dev/null
@@ -1,28 +0,0 @@
-# [PROJECT NAME] Development Guidelines
-
-Auto-generated from all feature plans. Last updated: [DATE]
-
-## Active Technologies
-
-[EXTRACTED FROM ALL PLAN.MD FILES]
-
-## Project Structure
-
-```text
-[ACTUAL STRUCTURE FROM PLANS]
-```
-
-## Commands
-
-[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES]
-
-## Code Style
-
-[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE]
-
-## Recent Changes
-
-[LAST 3 FEATURES AND WHAT THEY ADDED]
-
-<!-- MANUAL ADDITIONS START -->
-<!-- MANUAL ADDITIONS END -->
diff --git a/templates/commands/plan.md b/templates/commands/plan.md
index 4f1e9ed295..04db94ffaa 100644
--- a/templates/commands/plan.md
+++ b/templates/commands/plan.md
@@ -11,9 +11,6 @@ handoffs:
 scripts:
   sh: scripts/bash/setup-plan.sh --json
   ps: scripts/powershell/setup-plan.ps1 -Json
-agent_scripts:
-  sh: scripts/bash/update-agent-context.sh __AGENT__
-  ps: scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 
 ## User Input
@@ -145,15 +142,11 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Skip if project is purely internal (build scripts, one-off tools, etc.)
 
 3. **Agent context update**:
-   - Run `{AGENT_SCRIPT}`
-   - These scripts detect which AI agent is in use
-   - Update the appropriate agent-specific context file
-   - Add only new technology from current plan
-   - Preserve manual additions between markers
+   - Update the plan reference between the `<!-- SPECKIT START -->` and `<!-- SPECKIT END -->` markers in `__CONTEXT_FILE__` to point to the plan file created in step 1 (the IMPL_PLAN path)
 
-**Output**: data-model.md, /contracts/*, quickstart.md, agent-specific file
+**Output**: data-model.md, /contracts/*, quickstart.md, updated agent context file
 
 ## Key rules
 
-- Use absolute paths
+- Use absolute paths for filesystem operations; use project-relative paths for references in documentation and agent context files
 - ERROR on gate failures or unresolved clarifications
diff --git a/tests/integrations/test_cli.py b/tests/integrations/test_cli.py
index bd73ccd664..04a91682e8 100644
--- a/tests/integrations/test_cli.py
+++ b/tests/integrations/test_cli.py
@@ -56,14 +56,19 @@ def test_integration_copilot_creates_files(self, tmp_path):
 
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == "copilot"
-        assert "scripts" in data
-        assert "update-context" in data["scripts"]
 
         opts = json.loads((project / ".specify" / "init-options.json").read_text(encoding="utf-8"))
         assert opts["integration"] == "copilot"
+        assert opts["context_file"] == ".github/copilot-instructions.md"
 
         assert (project / ".specify" / "integrations" / "copilot.manifest.json").exists()
-        assert (project / ".specify" / "integrations" / "copilot" / "scripts" / "update-context.sh").exists()
+
+        # Context section should be upserted into the copilot instructions file
+        ctx_file = project / ".github" / "copilot-instructions.md"
+        assert ctx_file.exists()
+        ctx_content = ctx_file.read_text(encoding="utf-8")
+        assert "<!-- SPECKIT START -->" in ctx_content
+        assert "<!-- SPECKIT END -->" in ctx_content
 
         shared_manifest = project / ".specify" / "integrations" / "speckit.manifest.json"
         assert shared_manifest.exists()
diff --git a/tests/integrations/test_integration_base_markdown.py b/tests/integrations/test_integration_base_markdown.py
index 3700d35de5..f22bb298b4 100644
--- a/tests/integrations/test_integration_base_markdown.py
+++ b/tests/integrations/test_integration_base_markdown.py
@@ -99,7 +99,23 @@ def test_templates_are_processed(self, tmp_path):
             assert "__AGENT__" not in content, f"{f.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{f.name} has unprocessed {{ARGS}}"
             assert "\nscripts:\n" not in content, f"{f.name} has unstripped scripts: block"
-            assert "\nagent_scripts:\n" not in content, f"{f.name} has unstripped agent_scripts: block"
+
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference this integration's context file."""
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        plan_file = i.commands_dest(tmp_path) / i.command_filename("plan")
+        assert plan_file.exists(), f"Plan file {plan_file} not created"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan command should reference {i.context_file!r} but it was not found in {plan_file.name}"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            f"Plan command has unprocessed __CONTEXT_FILE__ placeholder in {plan_file.name}"
+        )
 
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration(self.KEY)
@@ -132,30 +148,35 @@ def test_modified_file_survives_uninstall(self, tmp_path):
         assert modified_file.exists()
         assert modified_file in skipped
 
-    # -- Scripts ----------------------------------------------------------
-
-    def test_setup_installs_update_context_scripts(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
-        assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
+    # -- Context section ---------------------------------------------------
 
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
-
-    def test_sh_script_is_executable(self, tmp_path):
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists(), f"Context file {i.context_file} not created for {self.KEY}"
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+            assert "read the current plan" in content
+
+    def test_teardown_removes_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        sh = tmp_path / ".specify" / "integrations" / self.KEY / "scripts" / "update-context.sh"
-        assert os.access(sh, os.X_OK)
+        m.save()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            # Add user content around the section
+            content = ctx_path.read_text(encoding="utf-8")
+            ctx_path.write_text("# My Rules\n\n" + content + "\n# Footer\n", encoding="utf-8")
+            i.teardown(tmp_path, m)
+            remaining = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" not in remaining
+            assert "<!-- SPECKIT END -->" not in remaining
+            assert "# My Rules" in remaining
 
     # -- CLI auto-promote -------------------------------------------------
 
@@ -203,6 +224,30 @@ def test_integration_flag_creates_files(self, tmp_path):
         commands = sorted(cmd_dir.glob("speckit.*"))
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the active integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"opts-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY, "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        i = get_integration(self.KEY)
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
+        )
+
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
@@ -220,10 +265,6 @@ def _expected_files(self, script_variant: str) -> list[str]:
         for stem in self.COMMAND_STEMS:
             files.append(f"{cmd_dir}/speckit.{stem}.md")
 
-        # Integration scripts
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.ps1")
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.sh")
-
         # Framework files
         files.append(f".specify/integration.json")
         files.append(f".specify/init-options.json")
@@ -232,14 +273,14 @@ def _expected_files(self, script_variant: str) -> list[str]:
 
         if script_variant == "sh":
             for name in ["check-prerequisites.sh", "common.sh", "create-new-feature.sh",
-                         "setup-plan.sh", "update-agent-context.sh"]:
+                         "setup-plan.sh"]:
                 files.append(f".specify/scripts/bash/{name}")
         else:
             for name in ["check-prerequisites.ps1", "common.ps1", "create-new-feature.ps1",
-                         "setup-plan.ps1", "update-agent-context.ps1"]:
+                         "setup-plan.ps1"]:
                 files.append(f".specify/scripts/powershell/{name}")
 
-        for name in ["agent-file-template.md", "checklist-template.md",
+        for name in ["checklist-template.md",
                      "constitution-template.md", "plan-template.md",
                      "spec-template.md", "tasks-template.md"]:
             files.append(f".specify/templates/{name}")
@@ -248,6 +289,11 @@ def _expected_files(self, script_variant: str) -> list[str]:
         # Bundled workflow
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
+
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
+
         return sorted(files)
 
     def test_complete_file_inventory_sh(self, tmp_path):
diff --git a/tests/integrations/test_integration_base_skills.py b/tests/integrations/test_integration_base_skills.py
index 72d32278ba..c8c152a84b 100644
--- a/tests/integrations/test_integration_base_skills.py
+++ b/tests/integrations/test_integration_base_skills.py
@@ -173,6 +173,23 @@ def test_skill_body_has_content(self, tmp_path):
             body = parts[2].strip() if len(parts) >= 3 else ""
             assert len(body) > 0, f"{f} has empty body"
 
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan skill must reference this integration's context file."""
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        plan_file = i.skills_dest(tmp_path) / "speckit-plan" / "SKILL.md"
+        assert plan_file.exists(), f"Plan skill {plan_file} not created"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan skill should reference {i.context_file!r} but it was not found"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            "Plan skill has unprocessed __CONTEXT_FILE__ placeholder"
+        )
+
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
@@ -217,30 +234,34 @@ def test_pre_existing_skills_not_removed(self, tmp_path):
 
         assert (foreign_dir / "SKILL.md").exists(), "Foreign skill was removed"
 
-    # -- Scripts ----------------------------------------------------------
+    # -- Context section ---------------------------------------------------
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
-        assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
-
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists(), f"Context file {i.context_file} not created for {self.KEY}"
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+            assert "read the current plan" in content
+
+    def test_teardown_removes_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
-
-    def test_sh_script_is_executable(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        i.setup(tmp_path, m)
-        sh = tmp_path / ".specify" / "integrations" / self.KEY / "scripts" / "update-context.sh"
-        assert os.access(sh, os.X_OK)
+        m.save()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            content = ctx_path.read_text(encoding="utf-8")
+            ctx_path.write_text("# My Rules\n\n" + content + "\n# Footer\n", encoding="utf-8")
+            i.teardown(tmp_path, m)
+            remaining = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" not in remaining
+            assert "<!-- SPECKIT END -->" not in remaining
+            assert "# My Rules" in remaining
 
     # -- CLI auto-promote -------------------------------------------------
 
@@ -286,6 +307,30 @@ def test_integration_flag_creates_files(self, tmp_path):
         skills_dir = i.skills_dest(project)
         assert skills_dir.is_dir(), f"Skills directory {skills_dir} not created"
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the active integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"opts-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY, "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        i = get_integration(self.KEY)
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
+        )
+
     # -- IntegrationOption ------------------------------------------------
 
     def test_options_include_skills_flag(self):
@@ -316,8 +361,6 @@ def _expected_files(self, script_variant: str) -> list[str]:
             ".specify/init-options.json",
             ".specify/integration.json",
             f".specify/integrations/{self.KEY}.manifest.json",
-            f".specify/integrations/{self.KEY}/scripts/update-context.ps1",
-            f".specify/integrations/{self.KEY}/scripts/update-context.sh",
             ".specify/integrations/speckit.manifest.json",
             ".specify/memory/constitution.md",
         ]
@@ -328,7 +371,6 @@ def _expected_files(self, script_variant: str) -> list[str]:
                 ".specify/scripts/bash/common.sh",
                 ".specify/scripts/bash/create-new-feature.sh",
                 ".specify/scripts/bash/setup-plan.sh",
-                ".specify/scripts/bash/update-agent-context.sh",
             ]
         else:
             files += [
@@ -336,11 +378,9 @@ def _expected_files(self, script_variant: str) -> list[str]:
                 ".specify/scripts/powershell/common.ps1",
                 ".specify/scripts/powershell/create-new-feature.ps1",
                 ".specify/scripts/powershell/setup-plan.ps1",
-                ".specify/scripts/powershell/update-agent-context.ps1",
             ]
         # Templates
         files += [
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",
@@ -352,6 +392,9 @@ def _expected_files(self, script_variant: str) -> list[str]:
             ".specify/workflows/speckit/workflow.yml",
             ".specify/workflows/workflow-registry.json",
         ]
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
         return sorted(files)
 
     def test_complete_file_inventory_sh(self, tmp_path):
diff --git a/tests/integrations/test_integration_base_toml.py b/tests/integrations/test_integration_base_toml.py
index e80f9abc10..ca66b2123a 100644
--- a/tests/integrations/test_integration_base_toml.py
+++ b/tests/integrations/test_integration_base_toml.py
@@ -310,6 +310,23 @@ def test_toml_is_valid(self, tmp_path):
                 raise AssertionError(f"{f.name} is not valid TOML: {exc}") from exc
             assert "prompt" in parsed, f"{f.name} parsed TOML has no 'prompt' key"
 
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference this integration's context file."""
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        plan_file = i.commands_dest(tmp_path) / i.command_filename("plan")
+        assert plan_file.exists(), f"Plan file {plan_file} not created"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan command should reference {i.context_file!r} but it was not found in {plan_file.name}"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            f"Plan command has unprocessed __CONTEXT_FILE__ placeholder in {plan_file.name}"
+        )
+
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
@@ -341,37 +358,34 @@ def test_modified_file_survives_uninstall(self, tmp_path):
         assert modified_file.exists()
         assert modified_file in skipped
 
-    # -- Scripts ----------------------------------------------------------
-
-    def test_setup_installs_update_context_scripts(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
-        assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
+    # -- Context section ---------------------------------------------------
 
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
-
-    def test_sh_script_is_executable(self, tmp_path):
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists(), f"Context file {i.context_file} not created for {self.KEY}"
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+            assert "read the current plan" in content
+
+    def test_teardown_removes_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        sh = (
-            tmp_path
-            / ".specify"
-            / "integrations"
-            / self.KEY
-            / "scripts"
-            / "update-context.sh"
-        )
-        assert os.access(sh, os.X_OK)
+        m.save()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            content = ctx_path.read_text(encoding="utf-8")
+            ctx_path.write_text("# My Rules\n\n" + content + "\n# Footer\n", encoding="utf-8")
+            i.teardown(tmp_path, m)
+            remaining = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" not in remaining
+            assert "<!-- SPECKIT END -->" not in remaining
+            assert "# My Rules" in remaining
 
     # -- CLI auto-promote -------------------------------------------------
 
@@ -441,6 +455,30 @@ def test_integration_flag_creates_files(self, tmp_path):
         commands = sorted(cmd_dir.glob("speckit.*.toml"))
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the active integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"opts-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY, "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        i = get_integration(self.KEY)
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
+        )
+
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
@@ -465,10 +503,6 @@ def _expected_files(self, script_variant: str) -> list[str]:
         for stem in self.COMMAND_STEMS:
             files.append(f"{cmd_dir}/speckit.{stem}.toml")
 
-        # Integration scripts
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.ps1")
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.sh")
-
         # Framework files
         files.append(".specify/integration.json")
         files.append(".specify/init-options.json")
@@ -481,7 +515,6 @@ def _expected_files(self, script_variant: str) -> list[str]:
                 "common.sh",
                 "create-new-feature.sh",
                 "setup-plan.sh",
-                "update-agent-context.sh",
             ]:
                 files.append(f".specify/scripts/bash/{name}")
         else:
@@ -490,12 +523,10 @@ def _expected_files(self, script_variant: str) -> list[str]:
                 "common.ps1",
                 "create-new-feature.ps1",
                 "setup-plan.ps1",
-                "update-agent-context.ps1",
             ]:
                 files.append(f".specify/scripts/powershell/{name}")
 
         for name in [
-            "agent-file-template.md",
             "checklist-template.md",
             "constitution-template.md",
             "plan-template.md",
@@ -508,6 +539,11 @@ def _expected_files(self, script_variant: str) -> list[str]:
         # Bundled workflow
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
+
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
+
         return sorted(files)
 
     def test_complete_file_inventory_sh(self, tmp_path):
diff --git a/tests/integrations/test_integration_base_yaml.py b/tests/integrations/test_integration_base_yaml.py
index e4c31b3c88..08f088576c 100644
--- a/tests/integrations/test_integration_base_yaml.py
+++ b/tests/integrations/test_integration_base_yaml.py
@@ -189,6 +189,23 @@ def test_yaml_prompt_excludes_frontmatter(self, tmp_path, monkeypatch):
         assert "scripts:" not in parsed["prompt"]
         assert "---" not in parsed["prompt"]
 
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference this integration's context file."""
+        i = get_integration(self.KEY)
+        if not i.context_file:
+            return
+        m = IntegrationManifest(self.KEY, tmp_path)
+        i.setup(tmp_path, m)
+        plan_file = i.commands_dest(tmp_path) / i.command_filename("plan")
+        assert plan_file.exists(), f"Plan file {plan_file} not created"
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan command should reference {i.context_file!r} but it was not found in {plan_file.name}"
+        )
+        assert "__CONTEXT_FILE__" not in content, (
+            f"Plan command has unprocessed __CONTEXT_FILE__ placeholder in {plan_file.name}"
+        )
+
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
@@ -220,37 +237,34 @@ def test_modified_file_survives_uninstall(self, tmp_path):
         assert modified_file.exists()
         assert modified_file in skipped
 
-    # -- Scripts ----------------------------------------------------------
-
-    def test_setup_installs_update_context_scripts(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
-        assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
+    # -- Context section ---------------------------------------------------
 
-    def test_scripts_tracked_in_manifest(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
-
-    def test_sh_script_is_executable(self, tmp_path):
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists(), f"Context file {i.context_file} not created for {self.KEY}"
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+            assert "read the current plan" in content
+
+    def test_teardown_removes_context_section(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         i.setup(tmp_path, m)
-        sh = (
-            tmp_path
-            / ".specify"
-            / "integrations"
-            / self.KEY
-            / "scripts"
-            / "update-context.sh"
-        )
-        assert os.access(sh, os.X_OK)
+        m.save()
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            content = ctx_path.read_text(encoding="utf-8")
+            ctx_path.write_text("# My Rules\n\n" + content + "\n# Footer\n", encoding="utf-8")
+            i.teardown(tmp_path, m)
+            remaining = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" not in remaining
+            assert "<!-- SPECKIT END -->" not in remaining
+            assert "# My Rules" in remaining
 
     # -- CLI auto-promote -------------------------------------------------
 
@@ -320,6 +334,30 @@ def test_integration_flag_creates_files(self, tmp_path):
         commands = sorted(cmd_dir.glob("speckit.*.yaml"))
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the active integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"opts-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", self.KEY, "--script", "sh",
+                "--no-git", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        i = get_integration(self.KEY)
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
+        )
+
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
@@ -344,10 +382,6 @@ def _expected_files(self, script_variant: str) -> list[str]:
         for stem in self.COMMAND_STEMS:
             files.append(f"{cmd_dir}/speckit.{stem}.yaml")
 
-        # Integration scripts
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.ps1")
-        files.append(f".specify/integrations/{self.KEY}/scripts/update-context.sh")
-
         # Framework files
         files.append(".specify/integration.json")
         files.append(".specify/init-options.json")
@@ -360,7 +394,6 @@ def _expected_files(self, script_variant: str) -> list[str]:
                 "common.sh",
                 "create-new-feature.sh",
                 "setup-plan.sh",
-                "update-agent-context.sh",
             ]:
                 files.append(f".specify/scripts/bash/{name}")
         else:
@@ -369,12 +402,10 @@ def _expected_files(self, script_variant: str) -> list[str]:
                 "common.ps1",
                 "create-new-feature.ps1",
                 "setup-plan.ps1",
-                "update-agent-context.ps1",
             ]:
                 files.append(f".specify/scripts/powershell/{name}")
 
         for name in [
-            "agent-file-template.md",
             "checklist-template.md",
             "constitution-template.md",
             "plan-template.md",
@@ -387,6 +418,11 @@ def _expected_files(self, script_variant: str) -> list[str]:
         # Bundled workflow
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
+
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
+
         return sorted(files)
 
     def test_complete_file_inventory_sh(self, tmp_path):
diff --git a/tests/integrations/test_integration_catalog.py b/tests/integrations/test_integration_catalog.py
index 3d0a14acdc..6d82a6c390 100644
--- a/tests/integrations/test_integration_catalog.py
+++ b/tests/integrations/test_integration_catalog.py
@@ -285,7 +285,7 @@ def test_clear_cache(self, tmp_path):
         "commands": [
             {"name": "speckit.specify", "file": "templates/speckit.specify.md"},
         ],
-        "scripts": ["update-context.sh"],
+        "scripts": [],
     },
 }
 
@@ -305,7 +305,7 @@ def test_valid_descriptor(self, tmp_path):
         assert desc.description == "Integration for My Agent"
         assert desc.requires_speckit_version == ">=0.6.0"
         assert len(desc.commands) == 1
-        assert desc.scripts == ["update-context.sh"]
+        assert desc.scripts == []
 
     def test_missing_schema_version(self, tmp_path):
         data = {**VALID_DESCRIPTOR}
diff --git a/tests/integrations/test_integration_claude.py b/tests/integrations/test_integration_claude.py
index d3b01097fc..153983dcf4 100644
--- a/tests/integrations/test_integration_claude.py
+++ b/tests/integrations/test_integration_claude.py
@@ -62,19 +62,17 @@ def test_setup_creates_skill_files(self, tmp_path):
         assert parsed["disable-model-invocation"] is False
         assert parsed["metadata"]["source"] == "templates/commands/plan.md"
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         integration = get_integration("claude")
         manifest = IntegrationManifest("claude", tmp_path)
-        created = integration.setup(tmp_path, manifest, script_type="sh")
-
-        scripts_dir = tmp_path / ".specify" / "integrations" / "claude" / "scripts"
-        assert scripts_dir.is_dir()
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
-
-        tracked = {path.resolve().relative_to(tmp_path.resolve()).as_posix() for path in created}
-        assert ".specify/integrations/claude/scripts/update-context.sh" in tracked
-        assert ".specify/integrations/claude/scripts/update-context.ps1" in tracked
+        integration.setup(tmp_path, manifest, script_type="sh")
+
+        ctx_path = tmp_path / integration.context_file
+        assert ctx_path.exists()
+        content = ctx_path.read_text(encoding="utf-8")
+        assert "<!-- SPECKIT START -->" in content
+        assert "<!-- SPECKIT END -->" in content
+        assert "read the current plan" in content
 
     def test_ai_flag_auto_promotes_and_enables_skills(self, tmp_path):
         from typer.testing import CliRunner
diff --git a/tests/integrations/test_integration_copilot.py b/tests/integrations/test_integration_copilot.py
index 34a9d54945..642b1e5300 100644
--- a/tests/integrations/test_integration_copilot.py
+++ b/tests/integrations/test_integration_copilot.py
@@ -143,7 +143,20 @@ def test_templates_are_processed(self, tmp_path):
             assert "__AGENT__" not in content, f"{agent_file.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{agent_file.name} has unprocessed {{ARGS}}"
             assert "\nscripts:\n" not in content
-            assert "\nagent_scripts:\n" not in content
+
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference copilot's context file."""
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        copilot.setup(tmp_path, m)
+        plan_file = tmp_path / ".github" / "agents" / "speckit.plan.agent.md"
+        assert plan_file.exists()
+        content = plan_file.read_text(encoding="utf-8")
+        assert copilot.context_file in content, (
+            f"Plan command should reference {copilot.context_file!r}"
+        )
+        assert "__CONTEXT_FILE__" not in content
 
     def test_complete_file_inventory_sh(self, tmp_path):
         """Every file produced by specify init --integration copilot --script sh."""
@@ -181,18 +194,15 @@ def test_complete_file_inventory_sh(self, tmp_path):
             ".github/prompts/speckit.tasks.prompt.md",
             ".github/prompts/speckit.taskstoissues.prompt.md",
             ".vscode/settings.json",
+            ".github/copilot-instructions.md",
             ".specify/integration.json",
             ".specify/init-options.json",
             ".specify/integrations/copilot.manifest.json",
             ".specify/integrations/speckit.manifest.json",
-            ".specify/integrations/copilot/scripts/update-context.ps1",
-            ".specify/integrations/copilot/scripts/update-context.sh",
             ".specify/scripts/bash/check-prerequisites.sh",
             ".specify/scripts/bash/common.sh",
             ".specify/scripts/bash/create-new-feature.sh",
             ".specify/scripts/bash/setup-plan.sh",
-            ".specify/scripts/bash/update-agent-context.sh",
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",
@@ -243,18 +253,15 @@ def test_complete_file_inventory_ps(self, tmp_path):
             ".github/prompts/speckit.tasks.prompt.md",
             ".github/prompts/speckit.taskstoissues.prompt.md",
             ".vscode/settings.json",
+            ".github/copilot-instructions.md",
             ".specify/integration.json",
             ".specify/init-options.json",
             ".specify/integrations/copilot.manifest.json",
             ".specify/integrations/speckit.manifest.json",
-            ".specify/integrations/copilot/scripts/update-context.ps1",
-            ".specify/integrations/copilot/scripts/update-context.sh",
             ".specify/scripts/powershell/check-prerequisites.ps1",
             ".specify/scripts/powershell/common.ps1",
             ".specify/scripts/powershell/create-new-feature.ps1",
             ".specify/scripts/powershell/setup-plan.ps1",
-            ".specify/scripts/powershell/update-agent-context.ps1",
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",
diff --git a/tests/integrations/test_integration_cursor_agent.py b/tests/integrations/test_integration_cursor_agent.py
index 3384fdc14f..352a0475b5 100644
--- a/tests/integrations/test_integration_cursor_agent.py
+++ b/tests/integrations/test_integration_cursor_agent.py
@@ -1,5 +1,10 @@
 """Tests for CursorAgentIntegration."""
 
+from pathlib import Path
+
+from specify_cli.integrations import get_integration
+from specify_cli.integrations.manifest import IntegrationManifest
+
 from .test_integration_base_skills import SkillsIntegrationTests
 
 
@@ -11,6 +16,81 @@ class TestCursorAgentIntegration(SkillsIntegrationTests):
     CONTEXT_FILE = ".cursor/rules/specify-rules.mdc"
 
 
+class TestCursorMdcFrontmatter:
+    """Verify .mdc frontmatter handling in upsert/remove context section."""
+
+    def _setup(self, tmp_path: Path):
+        i = get_integration("cursor-agent")
+        m = IntegrationManifest("cursor-agent", tmp_path)
+        return i, m
+
+    def test_new_mdc_gets_frontmatter(self, tmp_path):
+        """A freshly created .mdc file includes alwaysApply: true."""
+        i, m = self._setup(tmp_path)
+        i.setup(tmp_path, m)
+        ctx = (tmp_path / i.context_file).read_text(encoding="utf-8")
+        assert ctx.startswith("---\n")
+        assert "alwaysApply: true" in ctx
+
+    def test_existing_mdc_without_frontmatter_gets_it(self, tmp_path):
+        """An existing .mdc without frontmatter gets it added."""
+        i, m = self._setup(tmp_path)
+        ctx_path = tmp_path / i.context_file
+        ctx_path.parent.mkdir(parents=True, exist_ok=True)
+        ctx_path.write_text("# User rules\n", encoding="utf-8")
+        i.upsert_context_section(tmp_path)
+        content = ctx_path.read_text(encoding="utf-8")
+        assert content.lstrip().startswith("---")
+        assert "alwaysApply: true" in content
+        assert "# User rules" in content
+
+    def test_existing_mdc_with_frontmatter_preserves_it(self, tmp_path):
+        """An existing .mdc with custom frontmatter is preserved."""
+        i, m = self._setup(tmp_path)
+        ctx_path = tmp_path / i.context_file
+        ctx_path.parent.mkdir(parents=True, exist_ok=True)
+        ctx_path.write_text(
+            "---\nalwaysApply: true\ncustomKey: hello\n---\n\n# Rules\n",
+            encoding="utf-8",
+        )
+        i.upsert_context_section(tmp_path)
+        content = ctx_path.read_text(encoding="utf-8")
+        assert "alwaysApply: true" in content
+        assert "customKey: hello" in content
+        assert "<!-- SPECKIT START -->" in content
+
+    def test_existing_mdc_wrong_alwaysapply_fixed(self, tmp_path):
+        """An .mdc with alwaysApply: false gets corrected."""
+        i, m = self._setup(tmp_path)
+        ctx_path = tmp_path / i.context_file
+        ctx_path.parent.mkdir(parents=True, exist_ok=True)
+        ctx_path.write_text(
+            "---\nalwaysApply: false\n---\n\n# Rules\n",
+            encoding="utf-8",
+        )
+        i.upsert_context_section(tmp_path)
+        content = ctx_path.read_text(encoding="utf-8")
+        assert "alwaysApply: true" in content
+        assert "alwaysApply: false" not in content
+
+    def test_upsert_idempotent_no_duplicate_frontmatter(self, tmp_path):
+        """Repeated upserts don't duplicate frontmatter."""
+        i, m = self._setup(tmp_path)
+        i.upsert_context_section(tmp_path)
+        i.upsert_context_section(tmp_path)
+        content = (tmp_path / i.context_file).read_text(encoding="utf-8")
+        assert content.count("alwaysApply") == 1
+
+    def test_remove_deletes_mdc_with_only_frontmatter(self, tmp_path):
+        """Removing the section from a Speckit-only .mdc deletes the file."""
+        i, m = self._setup(tmp_path)
+        i.upsert_context_section(tmp_path)
+        ctx_path = tmp_path / i.context_file
+        assert ctx_path.exists()
+        i.remove_context_section(tmp_path)
+        assert not ctx_path.exists()
+
+
 class TestCursorAgentAutoPromote:
     """--ai cursor-agent auto-promotes to integration path."""
 
diff --git a/tests/integrations/test_integration_forge.py b/tests/integrations/test_integration_forge.py
index 7affd0d160..613ede91c0 100644
--- a/tests/integrations/test_integration_forge.py
+++ b/tests/integrations/test_integration_forge.py
@@ -73,19 +73,16 @@ def test_setup_creates_md_files(self, tmp_path):
         for f in command_files:
             assert f.name.endswith(".md")
 
-    def test_setup_installs_update_scripts(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         from specify_cli.integrations.forge import ForgeIntegration
         forge = ForgeIntegration()
         m = IntegrationManifest("forge", tmp_path)
-        created = forge.setup(tmp_path, m)
-        script_files = [f for f in created if "scripts" in f.parts]
-        assert len(script_files) > 0
-        sh_script = tmp_path / ".specify" / "integrations" / "forge" / "scripts" / "update-context.sh"
-        ps_script = tmp_path / ".specify" / "integrations" / "forge" / "scripts" / "update-context.ps1"
-        assert sh_script in created
-        assert ps_script in created
-        assert sh_script.exists()
-        assert ps_script.exists()
+        forge.setup(tmp_path, m)
+        ctx_path = tmp_path / forge.context_file
+        assert ctx_path.exists()
+        content = ctx_path.read_text(encoding="utf-8")
+        assert "<!-- SPECKIT START -->" in content
+        assert "<!-- SPECKIT END -->" in content
 
     def test_all_created_files_tracked_in_manifest(self, tmp_path):
         from specify_cli.integrations.forge import ForgeIntegration
@@ -159,7 +156,20 @@ def test_templates_are_processed(self, tmp_path):
             assert "$ARGUMENTS" not in content, f"{cmd_file.name} has unprocessed $ARGUMENTS"
             # Frontmatter sections should be stripped
             assert "\nscripts:\n" not in content
-            assert "\nagent_scripts:\n" not in content
+
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference forge's context file."""
+        from specify_cli.integrations.forge import ForgeIntegration
+        forge = ForgeIntegration()
+        m = IntegrationManifest("forge", tmp_path)
+        forge.setup(tmp_path, m)
+        plan_file = tmp_path / ".forge" / "commands" / "speckit.plan.md"
+        assert plan_file.exists()
+        content = plan_file.read_text(encoding="utf-8")
+        assert forge.context_file in content, (
+            f"Plan command should reference {forge.context_file!r}"
+        )
+        assert "__CONTEXT_FILE__" not in content
 
     def test_forge_specific_transformations(self, tmp_path):
         """Test Forge-specific processing: name injection and handoffs stripping."""
diff --git a/tests/integrations/test_integration_generic.py b/tests/integrations/test_integration_generic.py
index 74034ef105..8ca32078b5 100644
--- a/tests/integrations/test_integration_generic.py
+++ b/tests/integrations/test_integration_generic.py
@@ -31,9 +31,9 @@ def test_config_requires_cli_false(self):
         i = get_integration("generic")
         assert i.config["requires_cli"] is False
 
-    def test_context_file_is_none(self):
+    def test_context_file_is_agents_md(self):
         i = get_integration("generic")
-        assert i.context_file is None
+        assert i.context_file == "AGENTS.md"
 
     # -- Options ----------------------------------------------------------
 
@@ -158,30 +158,31 @@ def test_different_commands_dirs(self, tmp_path):
             cmd_files = [f for f in created if "scripts" not in f.parts]
             assert len(cmd_files) > 0
 
-    # -- Scripts ----------------------------------------------------------
+    # -- Context section ---------------------------------------------------
 
-    def test_setup_installs_update_context_scripts(self, tmp_path):
+    def test_setup_upserts_context_section(self, tmp_path):
         i = get_integration("generic")
         m = IntegrationManifest("generic", tmp_path)
         i.setup(tmp_path, m, parsed_options={"commands_dir": ".custom/cmds"})
-        scripts_dir = tmp_path / ".specify" / "integrations" / "generic" / "scripts"
-        assert scripts_dir.is_dir(), "Scripts directory not created for generic"
-        assert (scripts_dir / "update-context.sh").exists()
-        assert (scripts_dir / "update-context.ps1").exists()
-
-    def test_scripts_tracked_in_manifest(self, tmp_path):
-        i = get_integration("generic")
-        m = IntegrationManifest("generic", tmp_path)
-        i.setup(tmp_path, m, parsed_options={"commands_dir": ".custom/cmds"})
-        script_rels = [k for k in m.files if "update-context" in k]
-        assert len(script_rels) >= 2
-
-    def test_sh_script_is_executable(self, tmp_path):
+        if i.context_file:
+            ctx_path = tmp_path / i.context_file
+            assert ctx_path.exists()
+            content = ctx_path.read_text(encoding="utf-8")
+            assert "<!-- SPECKIT START -->" in content
+            assert "<!-- SPECKIT END -->" in content
+
+    def test_plan_references_correct_context_file(self, tmp_path):
+        """The generated plan command must reference generic's context file."""
         i = get_integration("generic")
         m = IntegrationManifest("generic", tmp_path)
         i.setup(tmp_path, m, parsed_options={"commands_dir": ".custom/cmds"})
-        sh = tmp_path / ".specify" / "integrations" / "generic" / "scripts" / "update-context.sh"
-        assert os.access(sh, os.X_OK)
+        plan_file = tmp_path / ".custom" / "cmds" / "speckit.plan.md"
+        assert plan_file.exists()
+        content = plan_file.read_text(encoding="utf-8")
+        assert i.context_file in content, (
+            f"Plan command should reference {i.context_file!r}"
+        )
+        assert "__CONTEXT_FILE__" not in content
 
     # -- CLI --------------------------------------------------------------
 
@@ -198,6 +199,28 @@ def test_cli_generic_without_commands_dir_fails(self, tmp_path):
         # The integration path validates via setup()
         assert result.exit_code != 0
 
+    def test_init_options_includes_context_file(self, tmp_path):
+        """init-options.json must include context_file for the generic integration."""
+        import json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "opts-generic"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", "generic",
+                "--ai-commands-dir", ".myagent/commands",
+                "--script", "sh", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        assert opts.get("context_file") == "AGENTS.md"
+
     def test_complete_file_inventory_sh(self, tmp_path):
         """Every file produced by specify init --integration generic --ai-commands-dir ... --script sh."""
         from typer.testing import CliRunner
@@ -221,6 +244,7 @@ def test_complete_file_inventory_sh(self, tmp_path):
             for p in project.rglob("*") if p.is_file()
         )
         expected = sorted([
+            "AGENTS.md",
             ".myagent/commands/speckit.analyze.md",
             ".myagent/commands/speckit.checklist.md",
             ".myagent/commands/speckit.clarify.md",
@@ -233,16 +257,12 @@ def test_complete_file_inventory_sh(self, tmp_path):
             ".specify/init-options.json",
             ".specify/integration.json",
             ".specify/integrations/generic.manifest.json",
-            ".specify/integrations/generic/scripts/update-context.ps1",
-            ".specify/integrations/generic/scripts/update-context.sh",
             ".specify/integrations/speckit.manifest.json",
             ".specify/memory/constitution.md",
             ".specify/scripts/bash/check-prerequisites.sh",
             ".specify/scripts/bash/common.sh",
             ".specify/scripts/bash/create-new-feature.sh",
             ".specify/scripts/bash/setup-plan.sh",
-            ".specify/scripts/bash/update-agent-context.sh",
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",
@@ -279,6 +299,7 @@ def test_complete_file_inventory_ps(self, tmp_path):
             for p in project.rglob("*") if p.is_file()
         )
         expected = sorted([
+            "AGENTS.md",
             ".myagent/commands/speckit.analyze.md",
             ".myagent/commands/speckit.checklist.md",
             ".myagent/commands/speckit.clarify.md",
@@ -291,16 +312,12 @@ def test_complete_file_inventory_ps(self, tmp_path):
             ".specify/init-options.json",
             ".specify/integration.json",
             ".specify/integrations/generic.manifest.json",
-            ".specify/integrations/generic/scripts/update-context.ps1",
-            ".specify/integrations/generic/scripts/update-context.sh",
             ".specify/integrations/speckit.manifest.json",
             ".specify/memory/constitution.md",
             ".specify/scripts/powershell/check-prerequisites.ps1",
             ".specify/scripts/powershell/common.ps1",
             ".specify/scripts/powershell/create-new-feature.ps1",
             ".specify/scripts/powershell/setup-plan.ps1",
-            ".specify/scripts/powershell/update-agent-context.ps1",
-            ".specify/templates/agent-file-template.md",
             ".specify/templates/checklist-template.md",
             ".specify/templates/constitution-template.md",
             ".specify/templates/plan-template.md",
diff --git a/tests/test_agent_config_consistency.py b/tests/test_agent_config_consistency.py
index 9cfe1ddbc9..75e80fdf33 100644
--- a/tests/test_agent_config_consistency.py
+++ b/tests/test_agent_config_consistency.py
@@ -1,6 +1,5 @@
 """Consistency checks for agent configuration across runtime surfaces."""
 
-import re
 from pathlib import Path
 
 from specify_cli import AGENT_CONFIG, AI_ASSISTANT_ALIASES, AI_ASSISTANT_HELP
@@ -61,20 +60,6 @@ def test_devcontainer_kiro_installer_uses_pinned_checksum(self):
         assert "sha256sum -c -" in post_create_text
         assert "KIRO_SKIP_KIRO_INSTALLER_VERIFY" not in post_create_text
 
-    def test_agent_context_scripts_use_kiro_cli(self):
-        """Agent context scripts should advertise kiro-cli and not legacy q agent key."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "kiro-cli" in bash_text
-        assert "kiro-cli" in pwsh_text
-        assert "Amazon Q Developer CLI" not in bash_text
-        assert "Amazon Q Developer CLI" not in pwsh_text
-
     # --- Tabnine CLI consistency checks ---
 
     def test_runtime_config_includes_tabnine(self):
@@ -96,20 +81,6 @@ def test_extension_registrar_includes_tabnine(self):
         assert cfg["args"] == "{{args}}"
         assert cfg["extension"] == ".toml"
 
-    def test_agent_context_scripts_include_tabnine(self):
-        """Agent context scripts should support tabnine agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "tabnine" in bash_text
-        assert "TABNINE_FILE" in bash_text
-        assert "tabnine" in pwsh_text
-        assert "TABNINE_FILE" in pwsh_text
-
     def test_ai_help_includes_tabnine(self):
         """CLI help text for --ai should include tabnine."""
         assert "tabnine" in AI_ASSISTANT_HELP
@@ -132,18 +103,6 @@ def test_kimi_in_extension_registrar(self):
         assert kimi_cfg["dir"] == ".kimi/skills"
         assert kimi_cfg["extension"] == "/SKILL.md"
 
-    def test_kimi_in_powershell_validate_set(self):
-        """PowerShell update-agent-context script should include 'kimi' in ValidateSet."""
-        ps_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        validate_set_match = re.search(r"\[ValidateSet\(([^)]*)\)\]", ps_text)
-        assert validate_set_match is not None
-        validate_set_values = re.findall(r"'([^']+)'", validate_set_match.group(1))
-
-        assert "kimi" in validate_set_values
-
     def test_ai_help_includes_kimi(self):
         """CLI help text for --ai should include kimi."""
         assert "kimi" in AI_ASSISTANT_HELP
@@ -168,32 +127,6 @@ def test_trae_in_extension_registrar(self):
         assert trae_cfg["args"] == "$ARGUMENTS"
         assert trae_cfg["extension"] == "/SKILL.md"
 
-    def test_trae_in_agent_context_scripts(self):
-        """Agent context scripts should support trae agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "trae" in bash_text
-        assert "TRAE_FILE" in bash_text
-        assert "trae" in pwsh_text
-        assert "TRAE_FILE" in pwsh_text
-
-    def test_trae_in_powershell_validate_set(self):
-        """PowerShell update-agent-context script should include 'trae' in ValidateSet."""
-        ps_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        validate_set_match = re.search(r"\[ValidateSet\(([^)]*)\)\]", ps_text)
-        assert validate_set_match is not None
-        validate_set_values = re.findall(r"'([^']+)'", validate_set_match.group(1))
-
-        assert "trae" in validate_set_values
-
     def test_ai_help_includes_trae(self):
         """CLI help text for --ai should include trae."""
         assert "trae" in AI_ASSISTANT_HELP
@@ -219,32 +152,6 @@ def test_pi_in_extension_registrar(self):
         assert pi_cfg["args"] == "$ARGUMENTS"
         assert pi_cfg["extension"] == ".md"
 
-    def test_pi_in_powershell_validate_set(self):
-        """PowerShell update-agent-context script should include 'pi' in ValidateSet."""
-        ps_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        validate_set_match = re.search(r"\[ValidateSet\(([^)]*)\)\]", ps_text)
-        assert validate_set_match is not None
-        validate_set_values = re.findall(r"'([^']+)'", validate_set_match.group(1))
-
-        assert "pi" in validate_set_values
-
-    def test_agent_context_scripts_include_pi(self):
-        """Agent context scripts should support pi agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "pi" in bash_text
-        assert "Pi Coding Agent" in bash_text
-        assert "pi" in pwsh_text
-        assert "Pi Coding Agent" in pwsh_text
-
     def test_ai_help_includes_pi(self):
         """CLI help text for --ai should include pi."""
         assert "pi" in AI_ASSISTANT_HELP
@@ -267,20 +174,6 @@ def test_iflow_in_extension_registrar(self):
         assert cfg["iflow"]["format"] == "markdown"
         assert cfg["iflow"]["args"] == "$ARGUMENTS"
 
-    def test_iflow_in_agent_context_scripts(self):
-        """Agent context scripts should support iflow agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "iflow" in bash_text
-        assert "IFLOW_FILE" in bash_text
-        assert "iflow" in pwsh_text
-        assert "IFLOW_FILE" in pwsh_text
-
     def test_ai_help_includes_iflow(self):
         """CLI help text for --ai should include iflow."""
         assert "iflow" in AI_ASSISTANT_HELP
@@ -303,18 +196,6 @@ def test_goose_in_extension_registrar(self):
         assert cfg["goose"]["format"] == "yaml"
         assert cfg["goose"]["args"] == "{{args}}"
 
-    def test_goose_in_agent_context_scripts(self):
-        """Agent context scripts should support goose agent type."""
-        bash_text = (
-            REPO_ROOT / "scripts" / "bash" / "update-agent-context.sh"
-        ).read_text(encoding="utf-8")
-        pwsh_text = (
-            REPO_ROOT / "scripts" / "powershell" / "update-agent-context.ps1"
-        ).read_text(encoding="utf-8")
-
-        assert "goose" in bash_text
-        assert "goose" in pwsh_text
-
     def test_ai_help_includes_goose(self):
         """CLI help text for --ai should include goose."""
         assert "goose" in AI_ASSISTANT_HELP
diff --git a/tests/test_cursor_frontmatter.py b/tests/test_cursor_frontmatter.py
deleted file mode 100644
index 9f8c31ce10..0000000000
--- a/tests/test_cursor_frontmatter.py
+++ /dev/null
@@ -1,266 +0,0 @@
-"""
-Tests for Cursor .mdc frontmatter generation (issue #669).
-
-Verifies that update-agent-context.sh properly prepends YAML frontmatter
-to .mdc files so that Cursor IDE auto-includes the rules.
-"""
-
-import os
-import shutil
-import subprocess
-import textwrap
-
-import pytest
-
-from tests.conftest import requires_bash
-
-SCRIPT_PATH = os.path.join(
-    os.path.dirname(__file__),
-    os.pardir,
-    "scripts",
-    "bash",
-    "update-agent-context.sh",
-)
-
-EXPECTED_FRONTMATTER_LINES = [
-    "---",
-    "description: Project Development Guidelines",
-    'globs: ["**/*"]',
-    "alwaysApply: true",
-    "---",
-]
-
-requires_git = pytest.mark.skipif(
-    shutil.which("git") is None,
-    reason="git is not installed",
-)
-
-
-class TestScriptFrontmatterPattern:
-    """Static analysis — no git required."""
-
-    def test_create_new_has_mdc_frontmatter_logic(self):
-        """create_new_agent_file() must contain .mdc frontmatter logic."""
-        with open(SCRIPT_PATH, encoding="utf-8") as f:
-            content = f.read()
-        assert 'if [[ "$target_file" == *.mdc ]]' in content
-        assert "alwaysApply: true" in content
-
-    def test_update_existing_has_mdc_frontmatter_logic(self):
-        """update_existing_agent_file() must also handle .mdc frontmatter."""
-        with open(SCRIPT_PATH, encoding="utf-8") as f:
-            content = f.read()
-        # There should be two occurrences of the .mdc check — one per function
-        occurrences = content.count('if [[ "$target_file" == *.mdc ]]')
-        assert occurrences >= 2, (
-            f"Expected at least 2 .mdc frontmatter checks, found {occurrences}"
-        )
-
-    def test_powershell_script_has_mdc_frontmatter_logic(self):
-        """PowerShell script must also handle .mdc frontmatter."""
-        ps_path = os.path.join(
-            os.path.dirname(__file__),
-            os.pardir,
-            "scripts",
-            "powershell",
-            "update-agent-context.ps1",
-        )
-        with open(ps_path, encoding="utf-8") as f:
-            content = f.read()
-        assert "alwaysApply: true" in content
-        occurrences = content.count(r"\.mdc$")
-        assert occurrences >= 2, (
-            f"Expected at least 2 .mdc frontmatter checks in PS script, found {occurrences}"
-        )
-
-
-@requires_git
-@requires_bash
-class TestCursorFrontmatterIntegration:
-    """Integration tests using a real git repo."""
-
-    @pytest.fixture
-    def git_repo(self, tmp_path):
-        """Create a minimal git repo with the spec-kit structure."""
-        repo = tmp_path / "repo"
-        repo.mkdir()
-
-        # Init git repo
-        subprocess.run(
-            ["git", "init"], cwd=str(repo), capture_output=True, check=True
-        )
-        subprocess.run(
-            ["git", "config", "user.email", "test@test.com"],
-            cwd=str(repo),
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "config", "user.name", "Test"],
-            cwd=str(repo),
-            capture_output=True,
-            check=True,
-        )
-
-        # Create .specify dir with config
-        specify_dir = repo / ".specify"
-        specify_dir.mkdir()
-        (specify_dir / "config.yaml").write_text(
-            textwrap.dedent("""\
-                project_type: webapp
-                language: python
-                framework: fastapi
-                database: N/A
-            """)
-        )
-
-        # Create template
-        templates_dir = specify_dir / "templates"
-        templates_dir.mkdir()
-        (templates_dir / "agent-file-template.md").write_text(
-            "# [PROJECT NAME] Development Guidelines\n\n"
-            "Auto-generated from all feature plans. Last updated: [DATE]\n\n"
-            "## Active Technologies\n\n"
-            "[EXTRACTED FROM ALL PLAN.MD FILES]\n\n"
-            "## Project Structure\n\n"
-            "[ACTUAL STRUCTURE FROM PLANS]\n\n"
-            "## Development Commands\n\n"
-            "[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES]\n\n"
-            "## Coding Conventions\n\n"
-            "[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE]\n\n"
-            "## Recent Changes\n\n"
-            "[LAST 3 FEATURES AND WHAT THEY ADDED]\n"
-        )
-
-        # Create initial commit
-        subprocess.run(
-            ["git", "add", "-A"], cwd=str(repo), capture_output=True, check=True
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "init"],
-            cwd=str(repo),
-            capture_output=True,
-            check=True,
-        )
-
-        # Create a feature branch so CURRENT_BRANCH detection works
-        subprocess.run(
-            ["git", "checkout", "-b", "001-test-feature"],
-            cwd=str(repo),
-            capture_output=True,
-            check=True,
-        )
-
-        # Create a spec so the script detects the feature
-        spec_dir = repo / "specs" / "001-test-feature"
-        spec_dir.mkdir(parents=True)
-        (spec_dir / "plan.md").write_text(
-            "# Test Feature Plan\n\n"
-            "## Technology Stack\n\n"
-            "- Language: Python\n"
-            "- Framework: FastAPI\n"
-        )
-
-        return repo
-
-    def _run_update(self, repo, agent_type="cursor-agent"):
-        """Run update-agent-context.sh for a specific agent type."""
-        script = os.path.abspath(SCRIPT_PATH)
-        result = subprocess.run(
-            ["bash", script, agent_type],
-            cwd=str(repo),
-            capture_output=True,
-            text=True,
-            timeout=30,
-        )
-        return result
-
-    def test_new_mdc_file_has_frontmatter(self, git_repo):
-        """Creating a new .mdc file must include YAML frontmatter."""
-        result = self._run_update(git_repo)
-        assert result.returncode == 0, f"Script failed: {result.stderr}"
-
-        mdc_file = git_repo / ".cursor" / "rules" / "specify-rules.mdc"
-        assert mdc_file.exists(), "Cursor .mdc file was not created"
-
-        content = mdc_file.read_text()
-        lines = content.splitlines()
-
-        # First line must be the opening ---
-        assert lines[0] == "---", f"Expected frontmatter start, got: {lines[0]}"
-
-        # Check all frontmatter lines are present
-        for expected in EXPECTED_FRONTMATTER_LINES:
-            assert expected in content, f"Missing frontmatter line: {expected}"
-
-        # Content after frontmatter should be the template content
-        assert "Development Guidelines" in content
-
-    def test_existing_mdc_without_frontmatter_gets_it_added(self, git_repo):
-        """Updating an existing .mdc file that lacks frontmatter must add it."""
-        # First, create the file WITHOUT frontmatter (simulating pre-fix state)
-        cursor_dir = git_repo / ".cursor" / "rules"
-        cursor_dir.mkdir(parents=True, exist_ok=True)
-        mdc_file = cursor_dir / "specify-rules.mdc"
-        mdc_file.write_text(
-            "# repo Development Guidelines\n\n"
-            "Auto-generated from all feature plans. Last updated: 2025-01-01\n\n"
-            "## Active Technologies\n\n"
-            "- Python + FastAPI (main)\n\n"
-            "## Recent Changes\n\n"
-            "- main: Added Python + FastAPI\n"
-        )
-
-        result = self._run_update(git_repo)
-        assert result.returncode == 0, f"Script failed: {result.stderr}"
-
-        content = mdc_file.read_text()
-        lines = content.splitlines()
-
-        assert lines[0] == "---", f"Expected frontmatter start, got: {lines[0]}"
-        for expected in EXPECTED_FRONTMATTER_LINES:
-            assert expected in content, f"Missing frontmatter line: {expected}"
-
-    def test_existing_mdc_with_frontmatter_not_duplicated(self, git_repo):
-        """Updating an .mdc file that already has frontmatter must not duplicate it."""
-        cursor_dir = git_repo / ".cursor" / "rules"
-        cursor_dir.mkdir(parents=True, exist_ok=True)
-        mdc_file = cursor_dir / "specify-rules.mdc"
-
-        frontmatter = (
-            "---\n"
-            "description: Project Development Guidelines\n"
-            'globs: ["**/*"]\n'
-            "alwaysApply: true\n"
-            "---\n\n"
-        )
-        body = (
-            "# repo Development Guidelines\n\n"
-            "Auto-generated from all feature plans. Last updated: 2025-01-01\n\n"
-            "## Active Technologies\n\n"
-            "- Python + FastAPI (main)\n\n"
-            "## Recent Changes\n\n"
-            "- main: Added Python + FastAPI\n"
-        )
-        mdc_file.write_text(frontmatter + body)
-
-        result = self._run_update(git_repo)
-        assert result.returncode == 0, f"Script failed: {result.stderr}"
-
-        content = mdc_file.read_text()
-        # Count occurrences of the frontmatter delimiter
-        assert content.count("alwaysApply: true") == 1, (
-            "Frontmatter was duplicated"
-        )
-
-    def test_non_mdc_file_has_no_frontmatter(self, git_repo):
-        """Non-.mdc agent files (e.g., Claude) must NOT get frontmatter."""
-        result = self._run_update(git_repo, agent_type="claude")
-        assert result.returncode == 0, f"Script failed: {result.stderr}"
-
-        claude_file = git_repo / ".claude" / "CLAUDE.md"
-        if claude_file.exists():
-            content = claude_file.read_text()
-            assert not content.startswith("---"), (
-                "Non-mdc file should not have frontmatter"
-            )
diff --git a/tests/test_extension_skills.py b/tests/test_extension_skills.py
index c9d13382ab..89e8b4a8b8 100644
--- a/tests/test_extension_skills.py
+++ b/tests/test_extension_skills.py
@@ -396,11 +396,8 @@ def test_skill_registration_resolves_script_placeholders(self, project_dir, temp
             "description: Scripted plan command\n"
             "scripts:\n"
             "  sh: ../../scripts/bash/setup-plan.sh --json \"{ARGS}\"\n"
-            "agent_scripts:\n"
-            "  sh: ../../scripts/bash/update-agent-context.sh __AGENT__\n"
             "---\n\n"
             "Run {SCRIPT}\n"
-            "Then {AGENT_SCRIPT}\n"
             "Review templates/checklist.md and memory/constitution.md for __AGENT__.\n"
         )
 
@@ -409,11 +406,9 @@ def test_skill_registration_resolves_script_placeholders(self, project_dir, temp
 
         content = (skills_dir / "speckit-scripted-ext-plan" / "SKILL.md").read_text()
         assert "{SCRIPT}" not in content
-        assert "{AGENT_SCRIPT}" not in content
         assert "{ARGS}" not in content
         assert "__AGENT__" not in content
         assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-        assert ".specify/scripts/bash/update-agent-context.sh claude" in content
         assert ".specify/templates/checklist.md" in content
         assert ".specify/memory/constitution.md" in content
 
diff --git a/tests/test_extensions.py b/tests/test_extensions.py
index 460404d597..5379178afe 100644
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -1334,13 +1334,9 @@ def test_codex_skill_registration_resolves_script_placeholders(self, project_dir
 scripts:
   sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
   ps: ../../scripts/powershell/setup-plan.ps1 -Json
-agent_scripts:
-  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
-  ps: ../../scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 
 Run {SCRIPT}
-Then {AGENT_SCRIPT}
 Agent __AGENT__
 """
         )
@@ -1361,11 +1357,9 @@ def test_codex_skill_registration_resolves_script_placeholders(self, project_dir
 
         content = skill_file.read_text()
         assert "{SCRIPT}" not in content
-        assert "{AGENT_SCRIPT}" not in content
         assert "__AGENT__" not in content
         assert "{ARGS}" not in content
         assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-        assert ".specify/scripts/bash/update-agent-context.sh codex" in content
 
     def test_codex_skill_alias_frontmatter_matches_alias_name(self, project_dir, temp_dir):
         """Codex alias skills should render their own matching `name:` frontmatter."""
@@ -1451,13 +1445,9 @@ def test_codex_skill_registration_uses_fallback_script_variant_without_init_opti
 scripts:
   sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
   ps: ../../scripts/powershell/setup-plan.ps1 -Json
-agent_scripts:
-  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
-  ps: ../../scripts/powershell/update-agent-context.ps1 __AGENT__
 ---
 
 Run {SCRIPT}
-Then {AGENT_SCRIPT}
 """
         )
 
@@ -1474,13 +1464,10 @@ def test_codex_skill_registration_uses_fallback_script_variant_without_init_opti
 
         content = skill_file.read_text()
         assert "{SCRIPT}" not in content
-        assert "{AGENT_SCRIPT}" not in content
         if platform.system().lower().startswith("win"):
             assert ".specify/scripts/powershell/setup-plan.ps1 -Json" in content
-            assert ".specify/scripts/powershell/update-agent-context.ps1 codex" in content
         else:
             assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-            assert ".specify/scripts/bash/update-agent-context.sh codex" in content
 
     def test_codex_skill_registration_handles_non_dict_init_options(
         self, project_dir, temp_dir
@@ -1577,13 +1564,9 @@ def test_codex_skill_registration_fallback_prefers_powershell_on_windows(
 scripts:
   sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
   ps: ../../scripts/powershell/setup-plan.ps1 -Json
-agent_scripts:
-  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
-  ps: ../../scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 
 Run {SCRIPT}
-Then {AGENT_SCRIPT}
 """
         )
 
@@ -1599,7 +1582,6 @@ def test_codex_skill_registration_fallback_prefers_powershell_on_windows(
 
         content = skill_file.read_text()
         assert ".specify/scripts/powershell/setup-plan.ps1 -Json" in content
-        assert ".specify/scripts/powershell/update-agent-context.ps1 -AgentType codex" in content
         assert ".specify/scripts/bash/setup-plan.sh" not in content
 
     def test_register_commands_for_copilot(self, extension_dir, project_dir):
diff --git a/tests/test_presets.py b/tests/test_presets.py
index b883d554b0..35c19bdd7f 100644
--- a/tests/test_presets.py
+++ b/tests/test_presets.py
@@ -1648,7 +1648,6 @@ def test_url_cache_expired(self, project_dir):
     "tasks-template",
     "checklist-template",
     "constitution-template",
-    "agent-file-template",
 ]
 
 
@@ -2911,7 +2910,7 @@ def test_lean_command_files_exist(self):
             assert tmpl_path.exists(), f"Missing command file: {tmpl['file']}"
 
     def test_lean_commands_have_no_scripts(self):
-        """Verify lean commands have no scripts or agent_scripts in frontmatter."""
+        """Verify lean commands have no scripts in frontmatter."""
         from specify_cli.agents import CommandRegistrar
 
         for name in LEAN_COMMAND_NAMES:
@@ -2919,7 +2918,6 @@ def test_lean_commands_have_no_scripts(self):
             content = cmd_path.read_text()
             frontmatter, _ = CommandRegistrar.parse_frontmatter(content)
             assert "scripts" not in frontmatter, f"{name} should not have scripts in frontmatter"
-            assert "agent_scripts" not in frontmatter, f"{name} should not have agent_scripts in frontmatter"
 
     def test_lean_commands_have_no_hooks(self):
         """Verify lean commands do not contain extension hook boilerplate."""