fix: wire config.build.engine into pipeline and connection

[carlos-alm]

Summary

• openRepo() and openReadonlyWithNative() in connection.ts previously read process.env.CODEGRAPH_ENGINE directly, silently ignoring any engine value set via .codegraphrc.json. They now read loadConfig().build.engine, which already incorporates both the env-var path (via applyEnvOverrides) and the config-file path.
• initializeEngine() and setupPipeline() in pipeline.ts used ctx.opts.engine || 'auto', skipping config.build.engine. The priority chain is now ctx.opts.engine ?? ctx.config.build.engine ?? 'auto'. Config is loaded first in setupPipeline() so build.engine is available before the native-availability check.
• Fix a pre-existing Biome format warning in fn-impact.ts (unnecessary parentheses, carried in from the fix/issue-1587 merge).

Test plan

• TypeScript type check passes (npx tsc --noEmit)
• Lint passes (npm run lint)
• Graph classifier and role unit tests pass (npx vitest run tests/graph/classifiers tests/unit/roles.test.ts)
• All non-WASM tests pass (WASM grammar files are not available in the worktree — this is a known limitation, not a regression)

Closes #1596

[greptile-apps]

Greptile Summary

This PR fixes a silent engine-override gap where connection.ts read process.env.CODEGRAPH_ENGINE directly and pipeline.ts used ctx.opts.engine || 'auto', both bypassing any engine value set in .codegraphrc.json. All three call sites now use the unified priority chain opts.engine ?? config.build.engine ?? 'auto', which already incorporates the env-var path via applyEnvOverrides.

• connection.ts: openRepo() and openReadonlyWithNative() now call loadConfig().build.engine (cached, negligible overhead); openReadonlyWithNative gains an optional opts.engine escape hatch mirroring openRepo().
• pipeline.ts: loadConfig() is moved above the enginePref computation in setupPipeline() so config.build.engine is populated before the native-availability check and initializeEngine() reads it; || is replaced with ?? throughout the engine chain.
• fn-impact.ts: Parentheses lint fix only, no functional change.

Confidence Score: 5/5

Safe to merge — changes are narrowly scoped to wiring an existing config value into call sites that were previously ignoring it, with no new code paths or data mutations.

All three engine-selection sites now use the same priority chain; loadConfig() is cached so per-call overhead in connection.ts is negligible; moving loadConfig() earlier in setupPipeline() is safe because openDb/initSchema have no dependency on ctx.config; the ?? vs || change is type-safe given the TypeScript union type on engine.

No files require special attention.

Important Files Changed

Filename	Overview
src/db/connection.ts	Replaces direct process.env.CODEGRAPH_ENGINE reads with loadConfig().build.engine in both openRepo() and openReadonlyWithNative(); adds optional opts.engine to openReadonlyWithNative() for parity with openRepo().
src/domain/graph/builder/pipeline.ts	Moves ctx.config = loadConfig() before enginePref computation so .codegraphrc.json build.engine is visible; changes
src/domain/analysis/fn-impact.ts	Removes unnecessary parentheses around nullish-coalescing expression to fix Biome lint warning; no functional change.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[CLI / programmatic call] --> B{opts.engine set?}
    B -- yes --> E[use opts.engine]
    B -- no --> C[loadConfig / ctx.config]
    C --> D{config.build.engine set?}
    D -- yes --> E
    D -- no --> F[fallback: 'auto']
    E --> G{engine !== 'wasm'?}
    F --> G
    G -- yes --> H{isNativeAvailable?}
    H -- yes --> I[open NativeDatabase / rusqlite]
    H -- no --> J[open better-sqlite3]
    G -- no --> J

Loading

%%{init: {'theme': 'base', 'themeVariables': {"darkMode": true, "background": "#0d1117", "primaryColor": "#21262d", "primaryTextColor": "#e6edf3", "primaryBorderColor": "#8b949e", "lineColor": "#8b949e", "textColor": "#e6edf3", "edgeLabelBackground": "#161b22", "actorBkg": "#21262d", "actorBorder": "#8b949e", "actorTextColor": "#e6edf3", "actorLineColor": "#8b949e", "signalColor": "#8b949e", "signalTextColor": "#e6edf3", "noteBkgColor": "#373320", "noteBorderColor": "#d4a72c", "noteTextColor": "#f0e6c0", "labelBoxBkgColor": "#21262d", "labelBoxBorderColor": "#8b949e", "labelTextColor": "#e6edf3", "loopTextColor": "#e6edf3", "activationBkgColor": "#30363d", "activationBorderColor": "#8b949e"}}}%%
flowchart TD
    A[CLI / programmatic call] --> B{opts.engine set?}
    B -- yes --> E[use opts.engine]
    B -- no --> C[loadConfig / ctx.config]
    C --> D{config.build.engine set?}
    D -- yes --> E
    D -- no --> F[fallback: 'auto']
    E --> G{engine !== 'wasm'?}
    F --> G
    G -- yes --> H{isNativeAvailable?}
    H -- yes --> I[open NativeDatabase / rusqlite]
    H -- no --> J[open better-sqlite3]
    G -- no --> J

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_{Reviews (4): Last reviewed commit: "fix: add engine override param to openRe..." | Re-trigger Greptile}

[greptile-apps]

openReadonlyWithNative cannot accept a per-call engine override

openRepo() accepts opts.engine so callers can force 'wasm' for a specific operation, but openReadonlyWithNative() has no such escape hatch and always reads loadConfig().build.engine. Any future caller that needs --engine wasm for a query path (e.g. a benchmark or test harness) has no way to opt out of the native path through this function. Since this is a query-only surface the risk is low today, but the asymmetry may cause confusion if callers expect parity with openRepo().

Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!

[carlos-alm]

Fixed in f7606b6. Added an optional opts: { engine?: 'native' | 'wasm' | 'auto' } parameter to openReadonlyWithNative() (default {}), mirroring the openRepo() escape hatch. The priority chain is now opts.engine ?? loadConfig().build.engine ?? 'auto' — identical to openRepo(). All existing callers are unaffected (they pass no opts). TypeScript compiles cleanly; the change is purely additive.

[greptile-apps]

loadConfig() uses process.cwd(), not the DB's directory

Both openRepo() and openReadonlyWithNative() call loadConfig() without a rootDir argument, so they resolve .codegraphrc.json from process.cwd(). When a caller passes a customDbPath pointing to a different repository (e.g. codegraph query --db /other/project/.codegraph/graph.db), the engine setting from that project's config file is never consulted — only the CWD config is used. This was equally true of the previous process.env.CODEGRAPH_ENGINE approach (a process-wide variable), so it is not a regression, but it is worth documenting as a known gap if multi-repo support is planned.

[carlos-alm]

Not fixed in this PR — this is a pre-existing limitation that predates this change (the previous process.env.CODEGRAPH_ENGINE approach was equally process-wide). Tracked as #1605 for follow-up when multi-repo / --db hardening is planned.

[github-actions]

Codegraph Impact Analysis

4 functions changed → 42 callers affected across 32 files

• openRepo in src/db/connection.ts:370 (28 transitive callers)
• openReadonlyWithNative in src/db/connection.ts:427 (8 transitive callers)
• initializeEngine in src/domain/graph/builder/pipeline.ts:63 (4 transitive callers)
• setupPipeline in src/domain/graph/builder/pipeline.ts:173 (5 transitive callers)

[carlos-alm]

Addressed Greptile P2 findings:

• Finding 1 (line 433, openReadonlyWithNative engine override): Fixed in f7606b6. Added opts: { engine?: 'native' | 'wasm' | 'auto' } parameter (default {}), matching openRepo()'s escape hatch. Priority chain is now opts.engine ?? loadConfig().build.engine ?? 'auto' — identical to openRepo(). Backward-compatible; no callers updated. TypeScript compiles cleanly.

• Finding 2 (line 387, loadConfig() uses process.cwd()): Pre-existing limitation, not a regression from this PR — the prior process.env.CODEGRAPH_ENGINE approach was equally process-wide. Tracked as connection: loadConfig() uses process.cwd() instead of DB root when customDbPath is set #1605 for follow-up when --db / multi-repo support is hardened.

[carlos-alm]

@greptileai