diff --git a/AGENTS.md b/AGENTS.md
index 8686b2f..bcbcdc5 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -105,9 +105,10 @@ The release strategy is evidence before expansion:
 v0.3: evidence pack + assembly gate + provenance checksums
 v0.4: compare mode for many FASTA files
 v0.5: submission readiness gate
-v0.6: transcriptome profile
-v0.7: protein profile
-v0.8: reference-panel profile
+v0.6: workflow-compatible exit contract
+v0.7: transcriptome profile
+v0.8: protein profile
+v0.9: reference-panel profile
 later: MCP/tool-agent interface and optional local summaries
 ```
 
@@ -123,20 +124,20 @@ Default product boundaries:
 Recommended next big release:
 
 ```text
-v0.5 should make submission readiness concrete before adding broad new biological profiles.
+v0.6 should simplify workflow integration before adding broad new biological profiles.
 ```
 
 The next planned feature direction is:
 
 ```text
-Submission Readiness Gate: --gate submission with --submission-target generic|ncbi.
+Workflow-Compatible Exit Contract: successful reports exit 0; report fields carry QC status.
 ```
 
-This should stay FASTA-level and database-free. It should check identifier
-safety, duplicate first-token IDs, unsafe characters, long identifiers, gap-like
-N runs, high ambiguity, and tiny-record advisories. It must not claim repository
-acceptance, biological completeness, annotation correctness, or contamination
-confirmation.
+This should keep JSON and TSV as the source of truth. Successful report
+generation should exit `0`, including WARN and FAIL reports. Argument parsing
+errors should exit `2`; configuration, input-access, and runtime errors should
+exit `3`. Existing v0.5 workflow integrations should keep compatibility handling
+until v0.6 packages and containers are published.
 
 ## Collaboration Preference
 
diff --git a/Cargo.lock b/Cargo.lock
index fda743e..e718225 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -360,7 +360,7 @@ dependencies = [
 
 [[package]]
 name = "fastaguard"
-version = "0.5.0"
+version = "0.6.0"
 dependencies = [
  "anyhow",
  "assert_cmd",
diff --git a/Cargo.toml b/Cargo.toml
index b738db6..8a54f06 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "fastaguard"
-version = "0.5.0"
+version = "0.6.0"
 edition = "2021"
 license = "MIT"
 description = "FASTA preflight QC for assembly pipelines"
diff --git a/README.md b/README.md
index 7b14e13..bf8fd98 100644
--- a/README.md
+++ b/README.md
@@ -49,7 +49,7 @@ downstream tool.
 
 | Channel | Status |
 | --- | --- |
-| Source/package metadata | `v0.5.0` is the latest tagged source release |
+| Source/package metadata | This branch prepares `v0.6.0`; `v0.5.0` remains the latest tag |
 | GitHub release | v0.5 GitHub release binaries are built from the `v0.5.0` tag |
 | Bioconda | `v0.5.0` is live for Linux and macOS x86_64/ARM64 |
 | BioContainers | `v0.5.0` is live as a pinned workflow image |
@@ -123,6 +123,7 @@ fastaguard --version
 The `--gate pipeline` examples below require FastaGuard `v0.3.0` or newer.
 The `fastaguard compare` example requires FastaGuard `v0.4.0` or newer.
 The `--gate submission` example requires FastaGuard `v0.5.0` or newer.
+The conventional exit contract below starts with FastaGuard `v0.6.0`.
 
 Run the assembly preflight check:
 
@@ -142,10 +143,10 @@ fastaguard sample.fa --profile assembly --gate pipeline
 ```
 
 The `pipeline` gate is the v0.3 assembly preset for workflow stop/go decisions.
-It fails on duplicate IDs, invalid characters, invalid FASTA structure, and
-high-N content. GC and length outliers remain advisory by default because they
-are routing signals, not proof of contamination or misassembly. To make an
-advisory finding block a pipeline, add it explicitly with `--fail-on`.
+It marks duplicate IDs, invalid characters, invalid FASTA structure, and high-N
+content as blocking findings. GC and length outliers remain advisory by default
+because they are routing signals, not proof of contamination or misassembly. To
+mark an advisory finding as blocking, add it explicitly with `--fail-on`.
 
 v0.4 compare starter example:
 
@@ -197,15 +198,21 @@ Published BioContainers provides the v0.5 image for workflow engines:
 docker pull quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0
 ```
 
-Exit codes:
+Starting with FastaGuard v0.6.0, exit codes are:
 
 ```text
-0 = pass
-1 = warnings above configured threshold
-2 = hard QC failure
-3 = invalid input / tool error
+0 = command completed and requested outputs were written
+2 = argument parsing error
+3 = configuration, input-access, or runtime error
 ```
 
+QC PASS/WARN/FAIL decisions are recorded in the machine-readable outputs,
+especially `verdict.status`, `gate.status`, and `gate.blocking_findings`.
+Workflow engines should route on those fields instead of interpreting QC
+findings from the process exit code. Single-file TSV reports include
+`input_path`, `verdict`, and `gate_status`; compare TSV reports retain one row
+per input with its path and status fields.
+
 ## Product Thesis
 
 FASTA files are everywhere, but FASTA QC is fragmented across ad hoc scripts, `seqkit stats`, assembly QC tools, completeness tools, contamination workflows, and pipeline-specific checks. Each is useful, but none is the simple default first command for:
@@ -261,7 +268,7 @@ v0.2 expands the assembly preflight layer with:
 
 v0.3 adds the assembly gate contract:
 
-- `--gate pipeline` for default workflow blocking behavior
+- `--gate pipeline` for the default workflow gate policy
 - `gate.blocking_findings` for machine stop/go decisions
 - checksum provenance with `provenance.input_sha256`
 - explicit advisory findings for evidence that should route follow-up QC rather
@@ -285,6 +292,15 @@ v0.5 adds the submission-readiness gate:
 - boundaries that keep FastaGuard upstream of official validators, NCBI FCS,
   annotation validation, QUAST, BUSCO, BlobToolKit, and CheckM
 
+v0.6 makes report generation workflow-compatible:
+
+- successful report generation exits `0` for PASS, WARN, and FAIL reports
+- argument parsing errors exit `2`; configuration, input-access, and runtime
+  errors exit `3`
+- single-file TSV reports include `input_path` for downstream routing
+- workflows enforce QC policy from stable report fields instead of process
+  status
+
 ## Positioning
 
 FastaGuard should recommend deeper tools when they are appropriate:
@@ -324,6 +340,7 @@ FastaGuard catches FASTA-level assembly problems before expensive assembly QC.
 - [v0.5 submission readiness evidence](docs/evidence/fastaguard-v0.5-submission-readiness.md)
 - [v0.5 public evidence workflow](docs/evidence/fastaguard-v0.5-public-evidence.md)
 - [Packaging](docs/packaging.md)
+- [v0.6.0 release notes](docs/releases/v0.6.0.md)
 - [v0.5.0 release notes](docs/releases/v0.5.0.md)
 - [v0.4.0 release notes](docs/releases/v0.4.0.md)
 - [v0.3.0 release notes](docs/releases/v0.3.0.md)
diff --git a/docs/mvp-spec.md b/docs/mvp-spec.md
index aaf285d..9c8ddc9 100644
--- a/docs/mvp-spec.md
+++ b/docs/mvp-spec.md
@@ -150,13 +150,19 @@ Default WARN conditions:
 
 ## Exit Codes
 
+Starting with FastaGuard v0.6.0:
+
 ```text
-0 = pass
-1 = warnings above configured threshold
-2 = hard QC failure
-3 = invalid input / tool error
+0 = command completed and requested outputs were written
+2 = argument parsing error
+3 = configuration, input-access, or runtime error
 ```
 
+QC PASS/WARN/FAIL decisions are report fields, not process-failure signals.
+Pipelines should read `verdict.status`, `gate.status`, and
+`gate.blocking_findings` from JSON/TSV outputs. Single-file TSV reports include
+`input_path`, `verdict`, and `gate_status` for downstream routing.
+
 ## Success Criteria
 
 The first release is successful if:
@@ -164,7 +170,7 @@ The first release is successful if:
 - it validates huge FASTA files without loading full sequences into memory
 - it produces useful HTML, JSON, TSV, and MultiQC-compatible outputs
 - it catches invalid FASTA structure, duplicate IDs, invalid characters, and high-N content
-- it has deterministic, documented exit codes
+- it has deterministic, documented status fields and tool-error exit codes
 - it can be added to a Nextflow or Snakemake pipeline in under 5 minutes
 
 ## Implementation Status
@@ -174,5 +180,5 @@ The v0.1 assembly MVP is implemented as a Rust CLI with:
 - streaming FASTA parsing for plain and gzipped files
 - assembly metrics
 - explainable findings
-- deterministic verdict exit codes
+- deterministic verdict status fields
 - JSON, TSV, HTML, and MultiQC-compatible outputs
diff --git a/docs/output-contract.md b/docs/output-contract.md
index 72f9efc..5a2d11b 100644
--- a/docs/output-contract.md
+++ b/docs/output-contract.md
@@ -4,7 +4,7 @@
 
 FastaGuard should be pipeline-native from the first release.
 
-The output contract is as important as the HTML report. Pipeline authors need stable field names, deterministic behavior, documented exit codes, and versioned schemas.
+The output contract is as important as the HTML report. Pipeline authors need stable field names, deterministic behavior, documented tool-error exit codes, and versioned schemas.
 
 ## Artifacts
 
@@ -29,6 +29,23 @@ fastaguard_compare_mqc.json
 v0.5 adds submission-readiness gate fields to the same JSON, TSV, HTML,
 MultiQC, and compare artifacts. JSON remains the source of truth.
 
+v0.6 separates process execution from QC status. Successful report generation
+returns exit code `0` for PASS, WARN, and FAIL reports.
+
+## Process Exit Contract
+
+Starting with FastaGuard v0.6.0:
+
+```text
+0 = command completed and requested outputs were written
+2 = argument parsing error
+3 = configuration, input-access, or runtime error
+```
+
+Workflow engines should apply stop/go policy from `gate.status`,
+`gate.blocking_findings`, or `verdict.status`. Process status only indicates
+whether FastaGuard completed the requested command and reports.
+
 ## JSON Contract
 
 Example v0.3 shape:
@@ -416,7 +433,8 @@ Recommended first rows:
 
 ```text
 metric	value
-schema_version	0.3.0
+schema_version	0.5.0
+input_path	sample.fa
 profile	assembly
 verdict	FAIL
 gate_mode	pipeline
diff --git a/docs/packaging.md b/docs/packaging.md
index aafaea4..7d0a0c8 100644
--- a/docs/packaging.md
+++ b/docs/packaging.md
@@ -135,7 +135,7 @@ Keep future releases compatible with Bioconda expectations:
 - keep a single static-ish CLI binary target
 - keep deterministic tests and tiny fixtures
 - avoid runtime databases for early releases
-- maintain stable exit codes
+- keep process exit codes reserved for CLI/tool execution errors
 - maintain a versioned JSON Schema
 
 Bioconda recipe guidance checked for this setup:
diff --git a/docs/releases/v0.6.0.md b/docs/releases/v0.6.0.md
new file mode 100644
index 0000000..41c1066
--- /dev/null
+++ b/docs/releases/v0.6.0.md
@@ -0,0 +1,31 @@
+# FastaGuard v0.6.0
+
+## Workflow-Compatible Exit Contract
+
+FastaGuard now separates command execution from FASTA quality decisions.
+Successful report generation exits with code `0`, including reports whose
+verdict or gate status is `WARN` or `FAIL`. Argument parsing errors exit with
+code `2`, while configuration, input-access, and runtime errors exit with code
+`3`.
+
+QC decisions remain explicit in the report contract:
+
+- `verdict.status` records the overall PASS/WARN/FAIL result.
+- `gate.status` records the selected gate result.
+- `gate.blocking_findings` lists findings that should stop downstream work.
+- single-file TSV reports include `input_path`, `verdict`, and `gate_status`.
+- compare TSV reports retain one row per input with its path and status fields.
+
+This keeps JSON and TSV reports available to Nextflow, Snakemake, nf-core, and
+other workflow engines. Pipelines can publish the evidence first and apply
+their own stop/go policy downstream.
+
+## Migration
+
+Workflows that previously interpreted process exit codes `1` and `2` as WARN
+and FAIL should instead read `gate.status` or `verdict.status` from JSON or TSV.
+The repository includes `examples/workflows/check_fastaguard_gate.py` for
+workflows that need a separate enforcement step after reports are collected.
+
+The JSON schema and finding catalog remain at version `0.5.0` because their
+structures and finding semantics are unchanged in this release.
diff --git a/docs/roadmap.md b/docs/roadmap.md
index 361a3d9..4209fee 100644
--- a/docs/roadmap.md
+++ b/docs/roadmap.md
@@ -27,7 +27,7 @@ Capabilities:
 - GC-vs-length plot data and HTML plot
 - PASS / WARN / FAIL verdict
 - JSON, TSV, HTML, and MultiQC-compatible outputs
-- deterministic exit codes
+- deterministic report status fields
 
 ## v0.2: Assembly Trust + Pipeline Adoption
 
@@ -118,7 +118,25 @@ Development scope:
 - FastaGuard does not replace NCBI, ENA, DDBJ official validators or guarantee
   repository acceptance
 
-## v0.6: Transcriptome Profile
+## v0.6: Workflow-Compatible Exit Contract
+
+Goal:
+
+```text
+Separate command execution from FASTA quality decisions in workflow engines.
+```
+
+Development scope:
+
+- return exit code `0` whenever requested reports are written successfully,
+  including WARN and FAIL reports
+- reserve exit code `2` for argument parsing errors
+- reserve exit code `3` for configuration, input-access, and runtime errors
+- keep PASS/WARN/FAIL decisions in stable JSON and TSV report fields
+- include `input_path` in single-file TSV reports for downstream routing
+- document migration from legacy QC-derived process exit codes
+
+## v0.7: Transcriptome Profile
 
 Potential additions:
 
@@ -128,7 +146,7 @@ Potential additions:
 - extreme GC outliers
 - isoform-heavy warning heuristics
 
-## v0.7: Protein Profile
+## v0.8: Protein Profile
 
 Potential additions:
 
@@ -138,7 +156,7 @@ Potential additions:
 - low-complexity regions
 - suspicious nucleotide-looking proteins
 
-## v0.8: Reference Panel Profile
+## v0.9: Reference Panel Profile
 
 Potential additions:
 
diff --git a/docs/tool-landscape.md b/docs/tool-landscape.md
index 255d828..d98305f 100644
--- a/docs/tool-landscape.md
+++ b/docs/tool-landscape.md
@@ -56,7 +56,7 @@ Without FastaGuard, users typically combine several partial checks:
 - run QUAST for assembly metrics
 - run BUSCO for biological completeness
 - run BlobToolKit or taxonomy tooling for contamination exploration
-- rely on pipeline-specific assumptions for exit codes and report parsing
+- rely on pipeline-specific assumptions for report parsing and stop/go policy
 
 That works, but it is fragmented. The missing layer is a default, explainable,
 machine-readable FASTA preflight contract.
diff --git a/docs/use-cases.md b/docs/use-cases.md
index c8c3722..f77b4e2 100644
--- a/docs/use-cases.md
+++ b/docs/use-cases.md
@@ -56,11 +56,12 @@ spend time on bad input.
 ### Pipeline Gate For Workflow Engines
 
 FastaGuard gives Nextflow, Snakemake, nf-core, Galaxy, and institutional
-pipelines a simple PASS/WARN/FAIL decision with deterministic exit codes and
-structured evidence.
+pipelines a simple PASS/WARN/FAIL decision with structured evidence in JSON,
+TSV, HTML, and MultiQC-compatible outputs.
 
 Pipelines can stop early on hard FASTA failures, continue with warnings, or
-route samples to follow-up tools based on machine-readable findings.
+route samples to follow-up tools based on machine-readable fields such as
+`gate.status` and `gate.blocking_findings`.
 
 ### Batch Triage With Compare Mode
 
diff --git a/docs/vision-plan.md b/docs/vision-plan.md
index 0ae8b51..bed45ec 100644
--- a/docs/vision-plan.md
+++ b/docs/vision-plan.md
@@ -26,7 +26,7 @@ The release strategy is evidence before expansion.
 FastaGuard should not rush into many biological profiles until the assembly
 preflight contract is trusted. The product should earn adoption in this order:
 
-1. **Trust:** reproducible evidence, stable schemas, clear exit codes, installable packages.
+1. **Trust:** reproducible evidence, stable schemas, clear status fields, installable packages.
 2. **Integration:** Bioconda, BioContainers, MultiQC, Nextflow, Snakemake, Galaxy.
 3. **Scale:** compare mode for many FASTA files and batch pipeline reports.
 4. **Readiness depth:** submission-oriented preflight checks before official validators.
@@ -109,7 +109,25 @@ The v0.5 contract should make workflow routing explicit through `gate.mode`,
 `readiness.categories[id=submission]` record, while still pointing users to
 official validators for final repository-specific checks.
 
-### v0.6: Transcriptome Profile
+### v0.6: Workflow-Compatible Exit Contract
+
+Goal:
+
+```text
+Let workflows collect complete QC reports before applying their own stop/go policy.
+```
+
+Successful report generation should exit with code `0` for PASS, WARN, and FAIL
+reports. Argument parsing errors should use code `2`; configuration,
+input-access, and runtime errors should use code `3`. JSON and TSV remain the
+source of truth for `verdict.status`, `gate.status`, and blocking findings.
+
+Single-file TSV reports should include `input_path` alongside status fields so
+workflow engines can route samples without scraping logs or HTML. Existing
+workflow examples pinned to v0.5 should retain compatibility handling until a
+v0.6 package and container are published.
+
+### v0.7: Transcriptome Profile
 
 Goal:
 
@@ -129,7 +147,7 @@ FastaGuard should not claim transcriptome biological completeness. It should
 route users to transcriptome-specific completeness and annotation tools when
 needed.
 
-### v0.7: Protein Profile
+### v0.8: Protein Profile
 
 Goal:
 
@@ -148,7 +166,7 @@ Initial protein checks:
 Protein mode should be strict about alphabet validity and careful about biology:
 it should flag preflight problems, not infer functional correctness.
 
-### v0.8: Reference-Panel Profile
+### v0.9: Reference-Panel Profile
 
 Goal:
 
@@ -219,7 +237,7 @@ Required adoption qualities:
 - generated BioContainers image
 - stable JSON schema
 - deterministic outputs
-- clear exit codes
+- clear tool-error exit codes
 - MultiQC compatibility
 - Nextflow, nf-core, Snakemake, and Galaxy examples
 - small public evidence pack
@@ -239,12 +257,13 @@ Recommended sequence:
 v0.3: evidence pack + assembly gate + provenance checksums
 v0.4: compare mode for many FASTA files
 v0.5: submission readiness gate
-v0.6: transcriptome profile
-v0.7: protein profile
-v0.8: reference-panel profile
+v0.6: workflow-compatible exit contract
+v0.7: transcriptome profile
+v0.8: protein profile
+v0.9: reference-panel profile
 later: MCP/tool-agent interface and optional local summaries
 ```
 
 This path gives FastaGuard the best chance to become a default tool: prove the
-assembly gate first, scale to batches, make submission readiness concrete, then
-expand profiles.
+assembly gate first, scale to batches, make submission readiness concrete,
+simplify workflow integration, then expand profiles.
diff --git a/docs/workflow-readiness.md b/docs/workflow-readiness.md
index b466007..fbe9976 100644
--- a/docs/workflow-readiness.md
+++ b/docs/workflow-readiness.md
@@ -32,6 +32,12 @@ External upstream-style validation was run on 2026-07-03 in dedicated checkouts:
   PASS, WARN, FAIL, and invalid FASTA fixtures plus captured `exit_code`
   outputs.
 
+The v0.6 source contract removes QC-derived process failures: successfully
+written PASS, WARN, and FAIL reports all return exit code `0`. The pinned v0.5
+starters keep their compatibility capture until v0.6 packages and containers
+are published. After publication, upstream wrappers can remove that workaround
+and route directly from JSON or TSV status fields.
+
 ## Safe Order
 
 1. Run local repository tests first.
@@ -53,11 +59,11 @@ official submission validators. The default workflow pattern is:
 collect FASTA-level evidence -> apply stop/go policy -> route downstream tools
 ```
 
-For local fail-fast runs, `--gate pipeline` and `--gate submission` write JSON,
-TSV, HTML, and MultiQC-compatible evidence before returning a blocking exit
-code. Some workflow engines remove failed-job outputs by default, so production
-integrations should use a collect-then-gate pattern when evidence preservation
-matters. The important contract fields are:
+With the published v0.5 runtime, `--gate pipeline` and `--gate submission` write
+JSON, TSV, HTML, and MultiQC-compatible evidence before returning a QC-derived
+exit code. The pinned local starters capture that code so the evidence remains
+available, then leave stop/go enforcement to a downstream gate step. The
+important contract fields are:
 
 - `verdict.status`
 - `gate.mode`
diff --git a/examples/nextflow/main.nf b/examples/nextflow/main.nf
index efad50d..f98f526 100644
--- a/examples/nextflow/main.nf
+++ b/examples/nextflow/main.nf
@@ -14,8 +14,8 @@ process FASTAGUARD {
 
     script:
     """
-    # Fail-fast starter example: FastaGuard WARN exits 1 and FAIL exits 2.
-    # Depending on engine behavior, evidence may remain only in the work directory.
+    # FastaGuard writes PASS/WARN/FAIL decisions to JSON/TSV/HTML reports.
+    # Route downstream workflow steps by reading gate.status from JSON.
     fastaguard ${fasta} \
       --profile assembly \
       --gate pipeline \
@@ -32,6 +32,6 @@ workflow {
 
 // Compare mode starter pattern for v0.4 cohort triage:
 // fastaguard compare assemblies/*.fa --profile assembly --gate pipeline
-// This is local fail-fast starter guidance, not an upstream nf-core submission yet.
-// FastaGuard WARN exits 1 and FAIL exits 2; collect-then-gate wrappers can preserve
-// evidence in publish directories before applying workflow stop/go logic.
+// This is local starter guidance, not an upstream nf-core submission yet.
+// FastaGuard returns success when reports are written; collect-then-gate wrappers
+// can apply workflow stop/go logic from gate.status.
diff --git a/examples/nf-core/README.md b/examples/nf-core/README.md
index ac58df2..329a50b 100644
--- a/examples/nf-core/README.md
+++ b/examples/nf-core/README.md
@@ -26,6 +26,7 @@ Emitted outputs:
 - `json`
 - `tsv`
 - `mqc`
+- `exit_code`
 - `versions`
 
 The module assumes `fastaguard` is available on `PATH` when run without a
@@ -47,13 +48,12 @@ The command block is written for the v0.3 assembly gate and runs:
 fastaguard sample.fa --profile assembly --gate pipeline
 ```
 
-That gate contract blocks downstream workflow steps on duplicate IDs, invalid
-characters, invalid FASTA structure, and high-N content. Gate failures intentionally exit with code `2` after writing reports, so downstream workflow steps stop while the JSON/HTML evidence remains available.
-
-This is a local fail-fast starter example: FastaGuard WARN exits 1 and FAIL exits 2.
-Depending on workflow engine behavior, naive fail-fast runs may leave evidence
-only in the work directory. A production wrapper can use a collect-then-gate
-pattern to publish JSON/HTML/TSV/MultiQC evidence before applying stop/go logic.
+That gate contract marks duplicate IDs, invalid characters, invalid FASTA
+structure, and high-N content as blocking findings. The published v0.5.0
+runtime returns `1` for WARN and `2` for FAIL. This module captures that legacy
+status so JSON, HTML, TSV, and MultiQC evidence can be published; a downstream
+gate step should then enforce stop/go policy from `gate.status` or the captured
+exit code. Runtime errors with status `3` still fail the process.
 
 For v0.4 cohort triage, compare mode is a starter pattern:
 
@@ -75,9 +75,9 @@ Pipeline authors should route on:
 - `gate.blocking_findings`
 - `readiness.categories[id=submission]`
 
-This is local fail-fast starter guidance only. It is not yet an upstream nf-core
-module submission, and the Snakemake example is not yet an official wrapper
-submission.
+This is local collect-then-gate starter guidance only. It is not yet an
+upstream nf-core module submission, and the Snakemake example is not yet an
+official wrapper submission.
 
 Example include:
 
diff --git a/examples/reports/README.md b/examples/reports/README.md
index 2344658..8b28554 100644
--- a/examples/reports/README.md
+++ b/examples/reports/README.md
@@ -1,6 +1,6 @@
 # Example Reports
 
-These tiny examples show the current v0.5 output contract without requiring large datasets.
+These tiny examples show the current v0.6 output contract without requiring large datasets.
 
 ## Assembly Pass
 
@@ -41,4 +41,6 @@ cargo run -- testdata/problem_assembly.fa \
   --multiqc examples/reports/assembly_fail/fastaguard_mqc.json
 ```
 
-The command exits with code `2` because this example contains critical FASTA-level blockers. Inspect the JSON `gate` object and readiness categories to separate blocking findings from advisory findings.
+The command exits with code `0` after writing the FAIL report. Inspect the JSON
+`gate` object and readiness categories to separate blocking findings from
+advisory findings.
diff --git a/examples/reports/assembly_fail/fastaguard.json b/examples/reports/assembly_fail/fastaguard.json
index bc738c8..ba08540 100644
--- a/examples/reports/assembly_fail/fastaguard.json
+++ b/examples/reports/assembly_fail/fastaguard.json
@@ -2,7 +2,7 @@
   "schema_version": "0.5.0",
   "tool": {
     "name": "FastaGuard",
-    "version": "0.5.0"
+    "version": "0.6.0"
   },
   "input": {
     "path": "testdata/problem_assembly.fa",
diff --git a/examples/reports/assembly_fail/fastaguard.tsv b/examples/reports/assembly_fail/fastaguard.tsv
index 59d824c..6f9540a 100644
--- a/examples/reports/assembly_fail/fastaguard.tsv
+++ b/examples/reports/assembly_fail/fastaguard.tsv
@@ -1,5 +1,6 @@
 metric	value
 schema_version	0.5.0
+input_path	testdata/problem_assembly.fa
 profile	assembly
 verdict	FAIL
 gate_mode	none
diff --git a/examples/reports/assembly_fail/fastaguard_report.html b/examples/reports/assembly_fail/fastaguard_report.html
index 5e08b79..1e66cf3 100644
--- a/examples/reports/assembly_fail/fastaguard_report.html
+++ b/examples/reports/assembly_fail/fastaguard_report.html
@@ -579,7 +579,7 @@ <h2>JSON</h2>
   &quot;schema_version&quot;: &quot;0.5.0&quot;,
   &quot;tool&quot;: {
     &quot;name&quot;: &quot;FastaGuard&quot;,
-    &quot;version&quot;: &quot;0.5.0&quot;
+    &quot;version&quot;: &quot;0.6.0&quot;
   },
   &quot;input&quot;: {
     &quot;path&quot;: &quot;testdata/problem_assembly.fa&quot;,
diff --git a/examples/reports/assembly_pass/fastaguard.json b/examples/reports/assembly_pass/fastaguard.json
index 57ae492..37d4285 100644
--- a/examples/reports/assembly_pass/fastaguard.json
+++ b/examples/reports/assembly_pass/fastaguard.json
@@ -2,7 +2,7 @@
   "schema_version": "0.5.0",
   "tool": {
     "name": "FastaGuard",
-    "version": "0.5.0"
+    "version": "0.6.0"
   },
   "input": {
     "path": "testdata/valid_assembly.fa",
diff --git a/examples/reports/assembly_pass/fastaguard.tsv b/examples/reports/assembly_pass/fastaguard.tsv
index b858d05..3e1c88a 100644
--- a/examples/reports/assembly_pass/fastaguard.tsv
+++ b/examples/reports/assembly_pass/fastaguard.tsv
@@ -1,5 +1,6 @@
 metric	value
 schema_version	0.5.0
+input_path	testdata/valid_assembly.fa
 profile	assembly
 verdict	WARN
 gate_mode	none
diff --git a/examples/reports/assembly_pass/fastaguard_report.html b/examples/reports/assembly_pass/fastaguard_report.html
index fbc1b28..312d0fd 100644
--- a/examples/reports/assembly_pass/fastaguard_report.html
+++ b/examples/reports/assembly_pass/fastaguard_report.html
@@ -201,7 +201,7 @@ <h2>JSON</h2>
   &quot;schema_version&quot;: &quot;0.5.0&quot;,
   &quot;tool&quot;: {
     &quot;name&quot;: &quot;FastaGuard&quot;,
-    &quot;version&quot;: &quot;0.5.0&quot;
+    &quot;version&quot;: &quot;0.6.0&quot;
   },
   &quot;input&quot;: {
     &quot;path&quot;: &quot;testdata/valid_assembly.fa&quot;,
diff --git a/examples/snakemake/Snakefile b/examples/snakemake/Snakefile
index 0c85bb2..b0f0bb0 100644
--- a/examples/snakemake/Snakefile
+++ b/examples/snakemake/Snakefile
@@ -8,8 +8,8 @@ rule fastaguard:
         multiqc="fastaguard_mqc.json"
     shell:
         """
-        # Fail-fast starter example: FastaGuard WARN exits 1 and FAIL exits 2.
-        # Depending on engine behavior, evidence may remain only in the work directory.
+        # FastaGuard writes PASS/WARN/FAIL decisions to JSON/TSV/HTML reports.
+        # Route downstream workflow steps by reading gate.status from JSON.
         fastaguard {input.fasta} \
           --profile assembly \
           --gate pipeline \
@@ -21,6 +21,6 @@ rule fastaguard:
 
 # Compare mode starter pattern for v0.4 cohort triage:
 # fastaguard compare assemblies/*.fa --profile assembly --gate pipeline
-# This is local fail-fast starter guidance, not an official Snakemake submission yet.
-# FastaGuard WARN exits 1 and FAIL exits 2; collect-then-gate wrappers can preserve
-# evidence in publish directories before applying workflow stop/go logic.
+# This is local starter guidance, not an official Snakemake submission yet.
+# FastaGuard returns success when reports are written; collect-then-gate wrappers
+# can apply workflow stop/go logic from gate.status.
diff --git a/src/cli.rs b/src/cli.rs
index 8eaca73..6fd2467 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -83,7 +83,7 @@ pub struct AnalysisArgs {
     #[arg(long, default_value = "assembly")]
     pub profile: String,
 
-    /// Gate preset for pipeline-friendly failure behavior.
+    /// Gate preset for report blocking policy.
     #[arg(long, value_enum, default_value_t = GateMode::None)]
     pub gate: GateMode,
 
@@ -91,7 +91,7 @@ pub struct AnalysisArgs {
     #[arg(long, value_enum)]
     pub submission_target: Option<SubmissionTarget>,
 
-    /// Comma-separated rule IDs that should fail the run when triggered.
+    /// Comma-separated rule IDs that mark the report as FAIL when triggered.
     #[arg(long, value_delimiter = ',')]
     pub fail_on: Vec<String>,
 
diff --git a/src/compare.rs b/src/compare.rs
index 7de89f0..e38c989 100644
--- a/src/compare.rs
+++ b/src/compare.rs
@@ -20,7 +20,6 @@ pub fn run_compare(config: CompareConfig) -> Result<i32> {
     }
 
     let summary = compare_summary(&samples);
-    let worst = worst_status(samples.iter().map(|sample| sample.gate_status));
     let cohort_findings = cohort_findings(&samples);
     let report = CompareReport {
         schema_version: SCHEMA_VERSION.to_string(),
@@ -39,7 +38,7 @@ pub fn run_compare(config: CompareConfig) -> Result<i32> {
     };
 
     crate::report::write_compare_all(&report, &config.outputs)?;
-    Ok(exit_code(worst))
+    Ok(0)
 }
 
 fn validate_unique_sample_ids(inputs: &[std::path::PathBuf]) -> Result<()> {
@@ -244,27 +243,6 @@ pub(crate) fn sample_id(path: &Path) -> String {
         .to_string()
 }
 
-pub(crate) fn worst_status<I>(statuses: I) -> VerdictStatus
-where
-    I: IntoIterator<Item = VerdictStatus>,
-{
-    statuses
-        .into_iter()
-        .fold(VerdictStatus::Pass, |worst, status| match (worst, status) {
-            (VerdictStatus::Fail, _) | (_, VerdictStatus::Fail) => VerdictStatus::Fail,
-            (VerdictStatus::Warn, _) | (_, VerdictStatus::Warn) => VerdictStatus::Warn,
-            _ => VerdictStatus::Pass,
-        })
-}
-
-fn exit_code(status: VerdictStatus) -> i32 {
-    match status {
-        VerdictStatus::Pass => 0,
-        VerdictStatus::Warn => 1,
-        VerdictStatus::Fail => 2,
-    }
-}
-
 fn usize_to_u64(value: usize) -> u64 {
     value.try_into().unwrap_or(u64::MAX)
 }
@@ -275,23 +253,6 @@ mod tests {
 
     use super::*;
 
-    #[test]
-    fn worst_status_prefers_fail_over_warn_over_pass() {
-        assert_eq!(
-            worst_status([
-                VerdictStatus::Pass,
-                VerdictStatus::Fail,
-                VerdictStatus::Warn
-            ]),
-            VerdictStatus::Fail
-        );
-        assert_eq!(
-            worst_status([VerdictStatus::Pass, VerdictStatus::Warn]),
-            VerdictStatus::Warn
-        );
-        assert_eq!(worst_status([VerdictStatus::Pass]), VerdictStatus::Pass);
-    }
-
     #[test]
     fn sample_id_uses_file_stem_without_compression_suffix() {
         assert_eq!(sample_id(Path::new("assemblies/ecoli.fa")), "ecoli");
diff --git a/src/lib.rs b/src/lib.rs
index 9b19c79..bbb596b 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -43,7 +43,7 @@ fn run_single(config: cli::RunConfig) -> Result<i32> {
     let outputs = config.outputs.clone();
     let output = build_single_report(config, run_started)?;
     report::write_all(&output, &outputs)?;
-    Ok(output.exit_code())
+    Ok(0)
 }
 
 pub(crate) fn build_single_report(
diff --git a/src/models.rs b/src/models.rs
index 3af5443..c30c5b9 100644
--- a/src/models.rs
+++ b/src/models.rs
@@ -521,14 +521,6 @@ impl FastaguardReport {
             },
         })
     }
-
-    pub fn exit_code(&self) -> i32 {
-        match self.verdict.status {
-            VerdictStatus::Pass => 0,
-            VerdictStatus::Warn => 1,
-            VerdictStatus::Fail => 2,
-        }
-    }
 }
 
 pub fn finding_actions(id: &str) -> Vec<FindingAction> {
diff --git a/src/report/tsv.rs b/src/report/tsv.rs
index da5d817..4c73ab4 100644
--- a/src/report/tsv.rs
+++ b/src/report/tsv.rs
@@ -12,6 +12,11 @@ pub fn write(report: &FastaguardReport, path: &Path) -> Result<()> {
 
     writeln!(writer, "metric\tvalue")?;
     write_metric(&mut writer, "schema_version", &report.schema_version)?;
+    write_metric(
+        &mut writer,
+        "input_path",
+        sanitize_tsv_value(&report.input.path),
+    )?;
     write_metric(&mut writer, "profile", &report.input.profile)?;
     write_metric(
         &mut writer,
@@ -210,6 +215,16 @@ fn write_metric(
     }
 }
 
+fn sanitize_tsv_value(value: &str) -> String {
+    value
+        .chars()
+        .map(|character| match character {
+            '\t' | '\r' | '\n' => ' ',
+            _ => character,
+        })
+        .collect()
+}
+
 fn affected_record_count(report: &FastaguardReport, finding_id: &str) -> u64 {
     report
         .findings
@@ -292,6 +307,40 @@ mod tests {
         assert!(output.contains("verdict\tWARN\n"), "{output}");
     }
 
+    #[test]
+    fn writes_input_path_for_downstream_routing() {
+        let report = test_report(VerdictStatus::Warn);
+        let file = NamedTempFile::new().unwrap();
+
+        write(&report, file.path()).unwrap();
+
+        let output = fs::read_to_string(file.path()).unwrap();
+        assert!(output.contains("input_path\tinput.fa\n"), "{output}");
+    }
+
+    #[test]
+    fn sanitizes_input_path_without_adding_tsv_rows() {
+        let mut report = test_report(VerdictStatus::Warn);
+        report.input.path = "inputs/sample\tone\n.fa".to_string();
+        let file = NamedTempFile::new().unwrap();
+
+        write(&report, file.path()).unwrap();
+
+        let output = fs::read_to_string(file.path()).unwrap();
+        assert!(
+            output.contains("input_path\tinputs/sample one .fa\n"),
+            "{output}"
+        );
+        assert_eq!(
+            output
+                .lines()
+                .filter(|line| line.starts_with("input_path\t"))
+                .count(),
+            1,
+            "{output}"
+        );
+    }
+
     #[test]
     fn writes_outlier_counts_from_matching_findings() {
         let mut report = test_report(VerdictStatus::Warn);
diff --git a/tests/cli.rs b/tests/cli.rs
index e917bef..7e9efca 100644
--- a/tests/cli.rs
+++ b/tests/cli.rs
@@ -17,6 +17,20 @@ fn help_mentions_preflight_positioning() {
         .stdout(predicate::str::contains("FASTA preflight QC"));
 }
 
+#[test]
+fn help_describes_gate_options_as_report_policy() {
+    let mut cmd = Command::cargo_bin("fastaguard").unwrap();
+    cmd.arg("--help")
+        .assert()
+        .success()
+        .stdout(predicate::str::contains(
+            "Gate preset for report blocking policy",
+        ))
+        .stdout(predicate::str::contains("mark the report as FAIL"))
+        .stdout(predicate::str::contains("failure behavior").not())
+        .stdout(predicate::str::contains("fail the run").not());
+}
+
 #[test]
 fn help_does_not_advertise_removed_warning_flag() {
     let removed_flag = ["--warn", "-on"].concat();
@@ -155,7 +169,7 @@ fn compare_writes_json_with_mixed_status_samples() {
     .arg("--multiqc")
     .arg(&multiqc)
     .assert()
-    .code(2)
+    .success()
     .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -219,7 +233,7 @@ fn compare_golden_mixed_status_matches() {
     .arg("--multiqc")
     .arg(&paths.multiqc)
     .assert()
-    .code(2)
+    .success()
     .stderr(predicate::str::contains("fastaguard error:").not());
 
     assert_json_matches_golden(&paths.json, "tests/golden/compare_mixed_status.json");
@@ -324,7 +338,7 @@ fn compare_includes_structurally_invalid_fasta_sample() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(2)
+    .success()
     .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -361,7 +375,7 @@ fn valid_assembly_writes_all_outputs_and_warns_for_terminal_ns() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(1)
+    .success()
     .stderr(predicate::str::is_empty());
 
     assert_all_outputs_exist(&outputs);
@@ -390,7 +404,7 @@ fn valid_report_includes_machine_summary_scope_and_provenance() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(1)
+    .success()
     .stderr(predicate::str::is_empty());
 
     let report = read_json(&outputs.json);
@@ -448,7 +462,7 @@ fn report_includes_v0_4_provenance_and_routing_hints() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(1);
+    .success();
 
     let report = read_json(&outputs.json);
     assert_eq!(report["schema_version"], json!("0.5.0"));
@@ -500,7 +514,7 @@ fn valid_report_includes_plot_contract() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(1)
+    .success()
     .stderr(predicate::str::is_empty());
 
     let report = read_json(&outputs.json);
@@ -557,7 +571,7 @@ fn gc_outlier_plot_flags_are_backed_by_warning_finding() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(1)
+        .success()
         .stderr(predicate::str::is_empty());
 
     let report = read_json(&outputs.json);
@@ -610,7 +624,7 @@ fn assembly_outliers_are_promoted_to_findings_without_fail_by_default() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(1)
+        .success()
         .stderr(predicate::str::is_empty());
 
     let report = read_json(&outputs.json);
@@ -705,14 +719,14 @@ fn valid_assembly_json_matches_golden_contract() {
     .arg("--multiqc")
     .arg(&paths.multiqc)
     .assert()
-    .code(1)
+    .success()
     .stderr(predicate::str::is_empty());
 
     assert_json_matches_golden(&paths.json, "tests/golden/valid_assembly.json");
 }
 
 #[test]
-fn problem_assembly_returns_failure_for_default_critical_findings() {
+fn problem_assembly_writes_failure_report_with_successful_process() {
     let temp_dir = TempDir::new().unwrap();
     let outputs = output_paths(&temp_dir, "problem");
 
@@ -726,7 +740,7 @@ fn problem_assembly_returns_failure_for_default_critical_findings() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(2)
+        .success()
         .stderr(predicate::str::contains("fastaguard error:").not());
 
     assert_all_outputs_exist(&outputs);
@@ -752,7 +766,7 @@ fn pipeline_gate_report_lists_blocking_and_advisory_findings() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(2)
+    .success()
     .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -809,7 +823,7 @@ fn report_includes_readiness_matrix() {
             multiqc.to_str().unwrap(),
         ])
         .assert()
-        .code(2);
+        .success();
 
     let report: serde_json::Value =
         serde_json::from_str(&std::fs::read_to_string(json).unwrap()).unwrap();
@@ -845,7 +859,7 @@ fn html_report_shows_gate_decision() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(2)
+    .success()
     .stderr(predicate::str::contains("fastaguard error:").not());
 
     let html = std::fs::read_to_string(&outputs.html).unwrap();
@@ -876,7 +890,7 @@ fn gate_none_report_preserves_warning_behavior_and_checksum() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(2)
+    .success()
     .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -920,7 +934,7 @@ fn problem_assembly_json_matches_golden_contract() {
         .arg("--multiqc")
         .arg(&paths.multiqc)
         .assert()
-        .code(2)
+        .success()
         .stderr(predicate::str::contains("fastaguard error:").not());
 
     assert_json_matches_golden(&paths.json, "tests/golden/problem_assembly.json");
@@ -941,7 +955,7 @@ fn problem_report_includes_structured_finding_actions() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(2)
+        .success()
         .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -985,7 +999,7 @@ fn problem_report_includes_v0_2_finding_taxonomy() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(2)
+        .success()
         .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -1011,7 +1025,7 @@ fn problem_report_includes_per_record_evidence() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(2)
+        .success()
         .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -1068,14 +1082,14 @@ fn invalid_fasta_json_matches_golden_contract() {
         .arg("--multiqc")
         .arg(&paths.multiqc)
         .assert()
-        .code(2)
+        .success()
         .stderr(predicate::str::contains("fastaguard error:").not());
 
     assert_json_matches_golden(&paths.json, "tests/golden/invalid_empty_record.json");
 }
 
 #[test]
-fn structurally_invalid_fasta_returns_failure_report() {
+fn structurally_invalid_fasta_writes_failure_report_with_successful_process() {
     let temp_dir = TempDir::new().unwrap();
     let input = temp_dir.path().join("invalid.fa");
     std::fs::write(&input, ">empty\n").unwrap();
@@ -1092,7 +1106,7 @@ fn structurally_invalid_fasta_returns_failure_report() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(2)
+        .success()
         .stderr(predicate::str::contains("fastaguard error:").not());
 
     assert_all_outputs_exist(&outputs);
@@ -1119,7 +1133,7 @@ fn invalid_fasta_report_includes_machine_contract_fields() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(2)
+        .success()
         .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -1171,7 +1185,7 @@ fn unknown_gate_value_is_cli_error() {
     let mut cmd = Command::cargo_bin("fastaguard").unwrap();
     cmd.args(["testdata/valid_assembly.fa", "--gate", "strict"])
         .assert()
-        .failure()
+        .code(2)
         .stderr(predicate::str::contains("invalid value 'strict'"));
 }
 
@@ -1209,7 +1223,7 @@ fn submission_gate_defaults_to_generic_target() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(1)
+    .success()
     .stderr(predicate::str::is_empty());
 
     let report = read_json(&outputs.json);
@@ -1242,7 +1256,7 @@ fn submission_target_ncbi_is_serialized_when_requested() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(1)
+    .success()
     .stderr(predicate::str::is_empty());
 
     let report = read_json(&outputs.json);
@@ -1280,7 +1294,7 @@ fn submission_gate_fails_identifier_hazards() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(2)
+    .success()
     .stderr(predicate::str::contains("fastaguard error:").not());
 
     let report = read_json(&outputs.json);
@@ -1336,7 +1350,7 @@ fn submission_gate_invalid_chars_fail_submission_readiness() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(2);
+        .success();
 
     let report = read_json(&outputs.json);
     let submission_readiness = report["readiness"]["categories"]
@@ -1378,7 +1392,7 @@ fn submission_identifier_hazards_route_to_official_validators_without_claiming_r
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(2);
+    .success();
 
     let report = read_json(&outputs.json);
     assert_routing_hint(
@@ -1415,7 +1429,7 @@ fn submission_gate_outputs_tsv_multiqc_and_html_fields() {
     .arg("--multiqc")
     .arg(&outputs.multiqc)
     .assert()
-    .code(2);
+    .success();
 
     let tsv = std::fs::read_to_string(&outputs.tsv).unwrap();
     assert!(tsv.contains("submission_target\tncbi\n"), "{tsv}");
@@ -1466,7 +1480,7 @@ fn compare_submission_gate_aggregates_submission_status() {
         .arg("--multiqc")
         .arg(&outputs.multiqc)
         .assert()
-        .code(2);
+        .success();
 
     let report = read_json(&outputs.json);
     assert_eq!(report["summary"]["submission_fail_count"], json!(1));
diff --git a/tests/golden/compare_all_pass.json b/tests/golden/compare_all_pass.json
index e149e03..13a5012 100644
--- a/tests/golden/compare_all_pass.json
+++ b/tests/golden/compare_all_pass.json
@@ -3,7 +3,7 @@
   "report_type": "compare",
   "tool": {
     "name": "FastaGuard",
-    "version": "0.5.0"
+    "version": "0.6.0"
   },
   "input": {
     "profile": "assembly",
diff --git a/tests/golden/compare_mixed_status.json b/tests/golden/compare_mixed_status.json
index 9f75bca..42ff95f 100644
--- a/tests/golden/compare_mixed_status.json
+++ b/tests/golden/compare_mixed_status.json
@@ -3,7 +3,7 @@
   "report_type": "compare",
   "tool": {
     "name": "FastaGuard",
-    "version": "0.5.0"
+    "version": "0.6.0"
   },
   "input": {
     "profile": "assembly",
diff --git a/tests/golden/invalid_empty_record.json b/tests/golden/invalid_empty_record.json
index 42c81e1..405559d 100644
--- a/tests/golden/invalid_empty_record.json
+++ b/tests/golden/invalid_empty_record.json
@@ -2,7 +2,7 @@
   "schema_version": "0.5.0",
   "tool": {
     "name": "FastaGuard",
-    "version": "0.5.0"
+    "version": "0.6.0"
   },
   "input": {
     "path": "testdata/invalid_empty_record.fa",
diff --git a/tests/golden/problem_assembly.json b/tests/golden/problem_assembly.json
index 0056662..49a7f2b 100644
--- a/tests/golden/problem_assembly.json
+++ b/tests/golden/problem_assembly.json
@@ -2,7 +2,7 @@
   "schema_version": "0.5.0",
   "tool": {
     "name": "FastaGuard",
-    "version": "0.5.0"
+    "version": "0.6.0"
   },
   "input": {
     "path": "testdata/problem_assembly.fa",
diff --git a/tests/golden/valid_assembly.json b/tests/golden/valid_assembly.json
index ba793f1..998471f 100644
--- a/tests/golden/valid_assembly.json
+++ b/tests/golden/valid_assembly.json
@@ -2,7 +2,7 @@
   "schema_version": "0.5.0",
   "tool": {
     "name": "FastaGuard",
-    "version": "0.5.0"
+    "version": "0.6.0"
   },
   "input": {
     "path": "testdata/valid_assembly.fa",
diff --git a/tests/python/test_adoption_assets.py b/tests/python/test_adoption_assets.py
index 2e872b8..3e65f9f 100644
--- a/tests/python/test_adoption_assets.py
+++ b/tests/python/test_adoption_assets.py
@@ -84,7 +84,8 @@ def test_v0_3_gate_examples_do_not_pin_v0_2_runtimes(self):
         )
         self.assertNotIn("fastaguard=0.2.0", wrapper_env)
         self.assertIn("--gate {gate}", wrapper_py)
-        self.assertIn("Gate failures intentionally exit with code `2`", nf_core_readme)
+        self.assertIn("published v0.5.0", nf_core_readme)
+        self.assertIn("captures that legacy", nf_core_readme)
         self.assertIn("fastaguard.exit_code", snakemake_readme)
 
     def test_v0_4_docs_explain_preflight_readiness_and_compare_mode(self):
@@ -125,9 +126,7 @@ def test_v0_4_examples_mention_compare_as_starter_pattern(self):
                 self.assertIn("fastaguard compare", text)
                 self.assertIn("starter", lower)
                 self.assertIn("local", lower)
-                self.assertIn("WARN exits 1", text)
-                self.assertIn("FAIL exits 2", text)
-                self.assertIn("fail-fast starter", lower)
+                self.assertIn("gate.status", text)
 
     def test_v0_5_submission_readiness_docs_are_present(self):
         readme = self.read("README.md")
diff --git a/tests/python/test_release_metadata.py b/tests/python/test_release_metadata.py
index 76e9dd4..984cd20 100644
--- a/tests/python/test_release_metadata.py
+++ b/tests/python/test_release_metadata.py
@@ -10,10 +10,10 @@
 
 
 class ReleaseMetadataTest(unittest.TestCase):
-    def test_package_targets_v0_5_0(self):
+    def test_package_targets_v0_6_0(self):
         cargo = tomllib.loads((ROOT / "Cargo.toml").read_text())
 
-        self.assertEqual(cargo["package"]["version"], "0.5.0")
+        self.assertEqual(cargo["package"]["version"], "0.6.0")
 
     def test_bioconda_recipe_tracks_published_v0_5_0_archive(self):
         recipe = (ROOT / "packaging" / "bioconda" / "meta.yaml").read_text()
@@ -53,6 +53,16 @@ def test_v0_5_0_release_notes_exist(self):
         self.assertIn("--gate submission", text)
         self.assertIn("--submission-target generic|ncbi", text)
 
+    def test_v0_6_0_release_notes_define_conventional_exit_contract(self):
+        notes = ROOT / "docs" / "releases" / "v0.6.0.md"
+
+        self.assertTrue(notes.exists())
+        text = notes.read_text()
+        self.assertIn("FastaGuard v0.6.0", text)
+        self.assertIn("Successful report generation exits with code `0`", text)
+        self.assertIn("`input_path`", text)
+        self.assertIn("`gate.status`", text)
+
     def test_bioconda_recipe_has_publishable_v0_5_0_source_sha(self):
         recipe = (ROOT / "packaging" / "bioconda" / "meta.yaml").read_text()
         marker = "REPLACE" + "_WITH_"
diff --git a/tests/schema_contract.rs b/tests/schema_contract.rs
index e38d661..74629f4 100644
--- a/tests/schema_contract.rs
+++ b/tests/schema_contract.rs
@@ -271,7 +271,7 @@ fn freshly_generated_outlier_report_validates_against_json_schema() {
         .arg("--multiqc")
         .arg(&multiqc)
         .assert()
-        .code(1);
+        .success();
 
     let schema = read_json(Path::new("schema/fastaguard.schema.json"));
     let report = read_json(&json);