fix: address quality issues in builder pipeline, config, and db connection handling

[carlos-alm]

Summary

• Fix a real correctness bug in src/infrastructure/config.ts: applyExcludeTestsShorthand mutated merged.query in place, corrupting the shared DEFAULTS.query object for the remainder of a long-running process (e.g. codegraph mcp --multi-repo) whenever a repo's .codegraphrc.json used the top-level excludeTests shorthand.
• Fix a resource-leak ordering bug in src/db/connection.ts's openReadonlyWithNative: it opened the SQLite handle before loadConfig, so a config error would leak the already-open handle. Reordered to match the correct pattern already used by openRepo.
• Add debug() logging to previously-silent/comment-only catch blocks across the builder pipeline and cli/commands/info.ts.
• Decompose buildChaContext into three focused builder functions.
• Split purgeAndAddReverseDeps and wire CODEGRAPH_FAST_SKIP_DIAG through config.
• Extract getOrCreateBatchStmt and dedupe batch-insert helpers in builder/helpers.ts.

Titan Audit Context

• Phase: quality_fix
• Domain: builder, config, db
• Commits: 6
• Depends on: PR Bump actions/github-script from 7 to 8 #3 (decompositions batch 1)

Changes

• src/infrastructure/config.ts, tests/unit/config.test.ts
• src/db/connection.ts, tests/unit/openReadonlyWithNative-leak.test.ts
• src/domain/graph/builder/{helpers,pipeline}.ts, src/domain/graph/builder/stages/{detect-changes,native-orchestrator}.ts, src/cli/commands/info.ts
• src/domain/graph/builder/cha.ts

Metrics Impact

Two of these are genuine production bugs (config-corruption-across-repos and a resource leak on config-error paths) found and fixed during the Titan GAUNTLET audit — both independently reproduced with standalone repros before the fix.

Test plan

• CI passes (lint + build + tests)
• codegraph check --cycles --boundaries passes
• No new functions above complexity thresholds

Closes #1725

[greptile-apps]

Greptile Summary

This PR fixes two genuine production bugs (DEFAULTS singleton mutation in loadConfig and a resource leak in openReadonlyWithNative), adds debug logging to previously-silent catch blocks, and decomposes several large functions into focused helpers.

• Config mutation fix: applyExcludeTestsShorthand previously wrote merged.query.excludeTests in place, poisoning the shared DEFAULTS.query reference across loadConfig calls in long-running processes. The fix applies copy-on-write semantics and also wraps DEFAULTS with deepFreeze and seeds loadConfig from structuredClone(DEFAULTS).
• Resource leak fix: openReadonlyWithNative previously opened the better-sqlite3 handle before calling resolveDbEngine/loadConfig; a config error would leave the handle dangling. The fix reorders so engine resolution runs first, mirroring the already-correct pattern in openRepo.
• Refactoring: buildChaContext is split into recordImplements/recordExtends/collectInstantiatedTypes; purgeAndAddReverseDeps is split into addReverseDeps + purgeStaleReverseDeps; getOrCreateBatchStmt deduplicates two identical WeakMap cache-getters.

Confidence Score: 5/5

Safe to merge — both targeted production bugs are correctly fixed, the refactoring preserves existing semantics, and each fix is backed by a focused regression test.

The config mutation fix (deepFreeze + structuredClone + copy-on-write) and the DB resource-leak reordering are straightforward and correct. The function decompositions preserve identical behavior — tracing the native vs WASM/JS call paths through the new helpers matches the original branch-by-branch. The new tests directly reproduce the described failure modes.

No files require special attention — all changes are targeted and backed by tests.

Important Files Changed

Filename	Overview
src/infrastructure/config.ts	Fixes the DEFAULTS mutation bug via deepFreeze + structuredClone + copy-on-write in applyExcludeTestsShorthand; extracts matchesAppliesTo to remove duplication between resolveConsent and promptForConsentIfNeeded.
src/db/connection.ts	Fixes resource leak by extracting resolveDbEngine and calling it before openReadonlyOrFail; eliminates duplicate rootDir derivation logic previously copy-pasted between openRepo and openReadonlyWithNative.
src/domain/graph/builder/stages/detect-changes.ts	Splits purgeAndAddReverseDeps into addReverseDeps + purgeStaleReverseDeps; wires fastSkipDiag through the function signature rather than reading process.env directly; adds debug logging to silent catch blocks.
src/domain/graph/builder/helpers.ts	Extracts getOrCreateBatchStmt and runBatchInsert to eliminate duplicate WeakMap cache-getter and chunk-loop logic between batchInsertNodes and batchInsertEdges; adds debug logging.
src/domain/graph/builder/cha.ts	Decomposes buildChaContext into recordImplements, recordExtends, and collectInstantiatedTypes; behavior is identical — pure structural refactoring.
src/domain/graph/builder/pipeline.ts	Passes fastSkipDiag from ctx.config through to detectNoChanges; adds debug logging to WASM tree cleanup catch blocks.
src/domain/graph/builder/stages/native-orchestrator.ts	Replaces silent catch blocks with debug()-level logging for WAL checkpoint, native DB close, WASM tree cleanup, and PRAGMA foreign_keys errors.
tests/unit/config.test.ts	Adds targeted regression tests for the DEFAULTS singleton leak: verifies excludeTests, build.engine, and llm.apiKey cannot bleed across loadConfig calls, and asserts DEFAULTS is deeply frozen.
tests/unit/openReadonlyWithNative-leak.test.ts	New regression test proving the resource-leak fix: uses a Proxy around the better-sqlite3 constructor to assert zero DB instances are created when loadConfig throws, and one instance is correctly closeable when it succeeds.
src/cli/commands/info.ts	Adds debug logging to the previously-silent catch block guarding the diagnostics section; no behavioral change.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[loadConfig called] --> B[structuredClone DEFAULTS - fresh mutable copy per call]
    B --> C[mergeConfig layers: global, repo, env]
    C --> D{excludeTests in rawLayer?}
    D -- yes --> E[copy-on-write: result.query = spread merged.query + excludeTests]
    D -- no --> F[pass through]
    E --> G[applyEnvOverrides / resolveSecrets]
    F --> G
    G --> H[return config - DEFAULTS unchanged]

    subgraph orn [openReadonlyWithNative - fixed ordering]
        I[resolveDbEngine called] --> J{engineOpt provided?}
        J -- yes --> K[return engineOpt - no loadConfig call]
        J -- no --> L[loadConfig called - may throw ConfigError]
        L -- throws --> M[function exits - no DB handle opened]
        L -- ok --> N[engine resolved]
        K --> N
        N --> O[openReadonlyOrFail - DB handle opened]
        O --> P[return db + nativeDb + close]
    end

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flowchart TD
    A[loadConfig called] --> B[structuredClone DEFAULTS - fresh mutable copy per call]
    B --> C[mergeConfig layers: global, repo, env]
    C --> D{excludeTests in rawLayer?}
    D -- yes --> E[copy-on-write: result.query = spread merged.query + excludeTests]
    D -- no --> F[pass through]
    E --> G[applyEnvOverrides / resolveSecrets]
    F --> G
    G --> H[return config - DEFAULTS unchanged]

    subgraph orn [openReadonlyWithNative - fixed ordering]
        I[resolveDbEngine called] --> J{engineOpt provided?}
        J -- yes --> K[return engineOpt - no loadConfig call]
        J -- no --> L[loadConfig called - may throw ConfigError]
        L -- throws --> M[function exits - no DB handle opened]
        L -- ok --> N[engine resolved]
        K --> N
        N --> O[openReadonlyOrFail - DB handle opened]
        O --> P[return db + nativeDb + close]
    end

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_{Reviews (2): Last reviewed commit: "fix: resolve merge conflicts with main (..." | Re-trigger Greptile}

[github-actions]

Codegraph Impact Analysis

37 functions changed → 173 callers affected across 102 files

• command.execute in src/cli/commands/info.ts:9 (0 transitive callers)
• execute in src/cli/commands/info.ts:9 (0 transitive callers)
• resolveDbEngine in src/db/connection.ts:361 (24 transitive callers)
• openRepo in src/db/connection.ts:410 (28 transitive callers)
• openReadonlyWithNative in src/db/connection.ts:465 (8 transitive callers)
• recordImplements in src/domain/graph/builder/cha.ts:37 (3 transitive callers)
• recordExtends in src/domain/graph/builder/cha.ts:52 (3 transitive callers)
• collectInstantiatedTypes in src/domain/graph/builder/cha.ts:75 (3 transitive callers)
• buildChaContext in src/domain/graph/builder/cha.ts:96 (3 transitive callers)
• readGitignorePatterns in src/domain/graph/builder/helpers.ts:101 (5 transitive callers)
• isSymlinkLoop in src/domain/graph/builder/helpers.ts:151 (2 transitive callers)
• getOrCreateBatchStmt in src/domain/graph/builder/helpers.ts:366 (14 transitive callers)
• getNodeStmt in src/domain/graph/builder/helpers.ts:385 (14 transitive callers)
• getEdgeStmt in src/domain/graph/builder/helpers.ts:395 (16 transitive callers)
• runBatchInsert in src/domain/graph/builder/helpers.ts:412 (16 transitive callers)
• batchInsertNodes in src/domain/graph/builder/helpers.ts:435 (8 transitive callers)
• batchInsertEdges in src/domain/graph/builder/helpers.ts:445 (13 transitive callers)
• runPipelineStages in src/domain/graph/builder/pipeline.ts:277 (5 transitive callers)
• buildGraph in src/domain/graph/builder/pipeline.ts:387 (5 transitive callers)
• getChangedFiles in src/domain/graph/builder/stages/detect-changes.ts:59 (3 transitive callers)