fix(embed): resolve default DB path from positional dir, not cwd

[carlos-alm]

Summary

codegraph embed [dir] and codegraph build [dir] resolved their default .codegraph/graph.db location inconsistently when --db was not passed: build correctly defaults to <dir>/.codegraph/graph.db, but embed ignored the positional dir argument entirely and instead searched upward from process.cwd() via findDbPath(undefined). This let embed silently attach to an unrelated graph.db sitting between cwd and the git root, or throw a confusing "no database found" error right after a successful build <dir>.

Fix

• findDbPath() and openReadonlyOrFail() (src/db/connection.ts) now accept an optional rootDirHint that anchors the default-path search at a known project root instead of process.cwd() — mirroring build's <rootDir>/.codegraph/graph.db convention while preserving the existing git-ceiling-aware upward search and all other findDbPath semantics. Both params are additive/optional, so every other call site (~30 across the codebase) is unaffected.
• buildEmbeddings() (src/domain/search/generator.ts) — the actual DB embed writes to — now passes its own rootDir parameter as that hint instead of defaulting to cwd.
• resolveStickyModel() (src/cli/commands/embed.ts), which does a pre-flight DB read to reuse a previously-stored embedding model, had the identical bug (calls openReadonlyOrFail(dbPath) with an undefined dbPath when --db isn't passed) and is fixed the same way.
• Updated the --db help text on embed to match build's documented default.

No native (Rust) changes — embed/buildEmbeddings is a TS-only search/CLI feature with no crates/codegraph-core equivalent.

Test plan

• Added a regression test in tests/search/embedding-strategy.test.ts that reproduces the exact repro from embed [dir] ignores positional dir for default DB path resolution (inconsistent with build) #1869: two unrelated directories each with their own graph.db, cwd set to one, buildEmbeddings(targetDir, ..., undefined) called on the other — asserts embeddings land in targetDir's DB and the cwd DB is never touched. Verified this test fails against the pre-fix code and passes after.
• Added unit coverage in tests/unit/db.test.ts for findDbPath's and openReadonlyOrFail's new rootDirHint parameter (wins over cwd, explicit --db still wins over the hint, unchanged default behavior when no hint is given).
• Added unit coverage in tests/unit/embed-command.test.ts verifying embed's execute() threads the resolved positional dir through to both the sticky-model lookup and buildEmbeddings.
• npm run lint — clean (only a pre-existing unrelated warning in a test fixture).
• npm run build — clean (tsc typecheck passes).
• npx vitest run tests/unit/db.test.ts tests/unit/embed-command.test.ts tests/search/embedding-strategy.test.ts — all 78 tests pass.
• npm test (full suite): 125 pre-existing failures, all in tests/parsers/* (missing optional WASM grammars not rebuilt in this worktree) and tests/integration/*/tests/benchmarks/* (missing native @optave/codegraph-darwin-arm64 addon in this worktree — node_modules here has no @optave/* packages at all). Confirmed none of the failing tests touch db/, search/, embed, or generator — this is a worktree-environment gap (in the spirit of worktree env: stale better-sqlite3 native binary + missing WASM grammars block npm test / titan-gate #1733), not a regression from this change.

Fixes #1869

Stacked on #1863 (base branch fix/issue-1863-resolvebyglobal-creates-a-call-edge-to-every) — only the embed/DB-path-resolution diff above is this issue's change.

[greptile-apps]

Greptile Summary

This PR fixes a path-resolution bug where codegraph embed [dir] was ignoring the positional dir argument when looking up the default DB location, instead walking up from process.cwd() — which could silently attach to an unrelated graph.db or produce a confusing "no database found" error after a successful build <dir>. The fix threads a rootDirHint parameter through findDbPath and openReadonlyOrFail so the search is anchored to the target directory, mirroring build's established convention.

• findDbPath and openReadonlyOrFail gain an optional rootDirHint that shifts the DB search start (and git-ceiling calculation) to the target project directory; all ~30 existing call sites are unaffected since the parameter is additive.
• buildEmbeddings and resolveStickyModel both pass rootDir as the hint, closing the original bug and the secondary resolveBusyTimeoutMs config-resolution bug (addressed in a prior review thread).
• Three new test suites cover the regression scenario, findDbPath/openReadonlyOrFail hint semantics, and the embed command's wiring end-to-end.

Confidence Score: 5/5

Safe to merge — the change is additive (new optional parameters, no call-site breakage) and directly addresses a well-understood path-resolution bug with targeted tests that fail on the pre-fix code.

The fix correctly threads rootDirHint through findDbPath and openReadonlyOrFail, the fallback priority (rootDirHint || ceiling || cwd) matches build's convention, and both previous review-thread issues (fallback ordering and resolveBusyTimeoutMs config derivation) are addressed. Three new test suites cover the regression end-to-end, the hint semantics, and the command wiring. All ~30 existing call sites are unaffected.

No files require special attention.

Important Files Changed

Filename	Overview
src/db/connection.ts	Adds optional rootDirHint to findDbPath and openReadonlyOrFail; also parameterises resolveDbSearchStartDir. Fallback base priority is correctly `rootDirHint
src/cli/commands/embed.ts	Threads root into both resolveStickyModel (which in turn passes it to openReadonlyOrFail as rootDirHint) and updates the --db help text. resolveBusyTimeoutMs(dbPath ?? rootDir) correctly loads config from the target project when no explicit --db is given, which is the fix from the second prior review thread.
src/domain/search/generator.ts	Single-line fix: findDbPath(undefined, rootDir) replaces findDbPath(undefined), anchoring DB resolution to the target directory. Clean and well-commented.
tests/search/embedding-strategy.test.ts	Adds a regression test reproducing issue #1869: two separate temp directories with their own DBs, cwd set to the unrelated one, verifies embeddings land in targetDir's DB and the cwd DB's schema is never modified. Solid integration coverage.
tests/unit/db.test.ts	Four new unit tests cover findDbPath hint vs cwd, explicit customPath override, unchanged default fallback, and the `rootDirHint
tests/unit/embed-command.test.ts	Adds mock for resolveBusyTimeoutMs and a new test asserting that openReadonlyOrFail and buildEmbeddings both receive path.resolve(targetDir) as their root argument when a positional dir is passed. Well-targeted unit coverage.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A["codegraph embed [dir]"] --> B["execute([dir], opts)"]
    B --> C["root = path.resolve(dir || '.')"]
    B --> D{"--db flag set?"}
    D -->|"yes: dbPath = opts.db"| E["resolveStickyModel(dbPath, root)"]
    D -->|"no: dbPath = undefined"| E
    E --> F["openReadonlyOrFail(dbPath, resolveBusyTimeoutMs(dbPath ?? root), root)"]
    F --> G["findDbPath(dbPath, rootDirHint=root)"]
    G --> H{"customPath set?"}
    H -->|yes| I["resolveCustomDbPath(dbPath)"]
    H -->|no| J["findRepoRoot(rootDirHint)"]
    J --> K["walkUpForDbPath(rootDirHint, ceiling)"]
    K -->|found| L["return existing DB path"]
    K -->|not found| M["base = rootDirHint || ceiling || cwd()"]
    M --> N["return base/.codegraph/graph.db"]
    B --> O["buildEmbeddings(root, model, dbPath, opts)"]
    O --> P["findDbPath(undefined, rootDir=root)"]
    P --> J

Loading

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flowchart TD
    A["codegraph embed [dir]"] --> B["execute([dir], opts)"]
    B --> C["root = path.resolve(dir || '.')"]
    B --> D{"--db flag set?"}
    D -->|"yes: dbPath = opts.db"| E["resolveStickyModel(dbPath, root)"]
    D -->|"no: dbPath = undefined"| E
    E --> F["openReadonlyOrFail(dbPath, resolveBusyTimeoutMs(dbPath ?? root), root)"]
    F --> G["findDbPath(dbPath, rootDirHint=root)"]
    G --> H{"customPath set?"}
    H -->|yes| I["resolveCustomDbPath(dbPath)"]
    H -->|no| J["findRepoRoot(rootDirHint)"]
    J --> K["walkUpForDbPath(rootDirHint, ceiling)"]
    K -->|found| L["return existing DB path"]
    K -->|not found| M["base = rootDirHint || ceiling || cwd()"]
    M --> N["return base/.codegraph/graph.db"]
    B --> O["buildEmbeddings(root, model, dbPath, opts)"]
    O --> P["findDbPath(undefined, rootDir=root)"]
    P --> J

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_{Reviews (5): Last reviewed commit: "fix(test): close DB handles in #1869 roo..." | Re-trigger Greptile}

[greptile-apps]

Fallback base prefers git root over rootDirHint

When walkUpForDbPath finds no existing DB, the fallback is ceiling || rootDirHint || process.cwd(). If rootDirHint sits inside a git repo (the common case), ceiling is the git root and wins — so the default DB path becomes <git-root>/.codegraph/graph.db rather than <rootDirHint>/.codegraph/graph.db. This diverges from build <dir>'s convention, which always writes to <dir>/.codegraph/graph.db. A user who runs codegraph embed /some/subproject before building will see an error pointing to the wrong location: No codegraph database found at <git-root>/.codegraph/graph.db instead of <rootDirHint>/.codegraph/graph.db. Swapping the order to rootDirHint || ceiling || process.cwd() would mirror build's behavior.

[carlos-alm]

Confirmed and fixed — swapped to rootDirHint || ceiling || cwd. Added a regression test that fails against the pre-fix priority order and passes after.

[greptile-apps]

resolveBusyTimeoutMs ignores rootDirHint — the same class of bug the PR fixes for the DB path.

When --db is not passed (dbPath is undefined), resolveBusyTimeoutMs(undefined) calls loadConfig(undefined), which loads db.busyTimeoutMs from process.cwd()'s config rather than the target root's config. If the project at root configures a non-default db.busyTimeoutMs, the sticky-model pre-flight read uses the wrong timeout. The fix is to pass root as the fallback rootDir when dbPath is absent.

Suggested change

	const db = openReadonlyOrFail(dbPath, resolveBusyTimeoutMs(dbPath), rootDir);
	const db = openReadonlyOrFail(dbPath, resolveBusyTimeoutMs(dbPath ?? rootDir), rootDir);

[carlos-alm]

Applied your suggested fix exactly.

[github-actions]

Codegraph Impact Analysis

7 functions changed → 136 callers affected across 83 files

• resolveStickyModel in src/cli/commands/embed.ts:14 (1 transitive callers)
• command.execute in src/cli/commands/embed.ts:70 (0 transitive callers)
• execute in src/cli/commands/embed.ts:70 (0 transitive callers)
• resolveDbSearchStartDir in src/db/connection.ts:310 (72 transitive callers)
• findDbPath in src/db/connection.ts:358 (112 transitive callers)
• openReadonlyOrFail in src/db/connection.ts:376 (115 transitive callers)
• buildEmbeddings in src/domain/search/generator.ts:222 (1 transitive callers)

[carlos-alm]

@greptileai