fix: recompute directory structure metrics for affected directories on incremental rebuild

[carlos-alm]

Summary

• The incremental build's "small fast path" (updateChangedFileMetrics, fires for ≤5 changed files on repos >20 files — i.e. almost every normal edit) only updated per-file node_metrics rows. It never touched directories at all: no directory-metrics recompute, no contains edge for a new file, no directory node for a brand-new directory. The non-fast-path incremental branch was already correct in both engines.
• Added refreshAffectedDirectoryMetrics/refresh_affected_directory_metrics (both engines) to the fast path: recomputes metrics for ancestor directories of touched files, lazily creates missing directory nodes/contains edges, and expands one hop via live import edges to catch cross-directory fan-in/fan-out shifts (mirrors the neighbor-expansion pattern classifyNodeRolesIncremental already uses for roles).

Closes #1738

Test plan

• npm test — full suite green (3444 passed, 0 failed)
• npm run lint / npx tsc --noEmit — clean
• cargo check / cargo test -p codegraph-core — clean
• Native addon rebuilt, codesigned, verified directly
• Drove the real buildGraph pipeline end-to-end (not just unit tests) on both engines: add-a-file, remove-a-file, new-nested-directory, and cross-directory-import scenarios, each diffed against an independent from-scratch full rebuild as ground truth
• Test validity confirmed by disabling each fix individually and observing the corresponding test(s) fail

Filed #1839 for a narrower residual gap (a directory whose only link to the touched set was via a file that was itself just removed — needs pre-purge capture logic, a materially larger separate change).

Stacked on #1837 (base branch fix/issue-1736-update-graph-hook-extensions) — only the structure/pipeline/constants/test diff is this issue's change.

[github-actions]

Codegraph Impact Analysis

3 functions changed → 8 callers affected across 3 files

• buildDirectoryStructure in src/domain/graph/builder/stages/build-structure.ts:51 (3 transitive callers)
• refreshAffectedDirectoryMetrics in src/domain/graph/builder/stages/build-structure.ts:293 (3 transitive callers)
• getAncestorDirs in src/shared/constants.ts:89 (6 transitive callers)

[greptile-apps]

Greptile Summary

This PR fixes a long-standing staleness bug (#1738) where the small-incremental fast path (updateChangedFileMetrics / update_changed_file_metrics) only updated per-file node_metrics rows and never touched directory nodes, contains edges, or directory-level aggregates. The fix adds refreshAffectedDirectoryMetrics / refresh_affected_directory_metrics to both the TypeScript and Rust engines, called immediately after the existing per-file update in the fast path.

• Core fix: recomputes fileCount, symbolCount, fanIn, fanOut, and cohesion for all ancestor directories of any added/removed/modified file, lazily creates missing directory nodes and contains edges for brand-new directories, and expands one hop via live import edges to catch cross-directory fan-in/fan-out shifts — seeded from leaf directories only (not the full ancestor chain) to avoid a 70-90 ms regression on near-root containers like src/.
• Rust pipeline plumbing: removed_files is threaded through run_structure_phase as a new parameter so the directory refresh covers deletions (zero re-parsed files still satisfies the ≤5 gate).
• getAncestorDirs promoted from a private helper in src/features/structure.ts to a shared export in src/shared/constants.ts, used by both the full rebuild path and the new fast-path refresh.

Confidence Score: 5/5

Safe to merge — the fast-path fix is well-scoped, both engines are updated in lockstep, and the integration tests validate all four key scenarios (add, remove, new nested dir, cross-directory fan-in) against independent full rebuilds as ground truth.

The change is additive: it only adds work to the fast path that the slow path already did correctly. The SQL metric formulas are verified to match the existing full-rebuild query in computeImportEdgeMaps. The one open finding is a stale inline comment in structure.rs (the Rust mirror of a comment already corrected in the TS side), which has no effect on behavior.

The stale comment in crates/codegraph-core/src/features/structure.rs (line 264) is the only item worth a second look; all other files are clean.

Important Files Changed

Filename	Overview
crates/codegraph-core/src/domain/graph/builder/pipeline.rs	Threads removed_files into run_structure_phase and calls refresh_affected_directory_metrics in the fast path — minimal, correct plumbing change.
crates/codegraph-core/src/features/structure.rs	Adds find_neighbor_files and refresh_affected_directory_metrics. Logic is correct and consistent with the TS mirror; one backwards inline comment (// 2. Wire dir -> parent-dir) that was fixed in the TS side was not updated here.
src/domain/graph/builder/stages/build-structure.ts	Calls refreshAffectedDirectoryMetrics after updateChangedFileMetrics in the fast path; SQL queries verified to match the full-rebuild metrics formula in src/features/structure.ts.
src/features/structure.ts	Removes the now-shared getAncestorDirs private function; no behavioral change, confirmed the remaining computeImportEdgeMaps query is consistent with the new incremental SQL.
src/shared/constants.ts	Promotes getAncestorDirs to a shared export with a widened Iterable<string> signature (backward-compatible for existing string[] callers).
tests/integration/issue-1738-structure-metrics-incremental.test.ts	Comprehensive regression suite with four scenarios (add file, remove file, brand-new nested dir, cross-directory fan-in shift); each diffs incremental output against an independent full rebuild as ground truth.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[Incremental build triggered] --> B{useSmallIncrementalFastPath?}
    B -- No --> C[Full / medium incremental structure rebuild]
    B -- Yes --> D[updateChangedFileMetrics\nper-file node_metrics rows]
    D --> E[refreshAffectedDirectoryMetrics\n— NEW —]
    E --> F[Collect ancestor dirs of\nchanged + removed files]
    F --> G[Expand via leaf-dir import edges\none hop to neighbor dirs]
    G --> H[DB transaction]
    H --> H1[1 · INSERT OR IGNORE directory nodes]
    H1 --> H2[2 · Wire parent→child contains edges]
    H2 --> H3[3 · Wire dir→file contains edges\nfor added/modified files]
    H3 --> H4[4 · Recompute fileCount / symbolCount\nfanIn / fanOut / cohesion per dir]
    H4 --> I[Commit]
    C --> I
    I --> J[Continue pipeline]

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flowchart TD
    A[Incremental build triggered] --> B{useSmallIncrementalFastPath?}
    B -- No --> C[Full / medium incremental structure rebuild]
    B -- Yes --> D[updateChangedFileMetrics\nper-file node_metrics rows]
    D --> E[refreshAffectedDirectoryMetrics\n— NEW —]
    E --> F[Collect ancestor dirs of\nchanged + removed files]
    F --> G[Expand via leaf-dir import edges\none hop to neighbor dirs]
    G --> H[DB transaction]
    H --> H1[1 · INSERT OR IGNORE directory nodes]
    H1 --> H2[2 · Wire parent→child contains edges]
    H2 --> H3[3 · Wire dir→file contains edges\nfor added/modified files]
    H3 --> H4[4 · Recompute fileCount / symbolCount\nfanIn / fanOut / cohesion per dir]
    H4 --> I[Commit]
    C --> I
    I --> J[Continue pipeline]

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_{Reviews (3): Last reviewed commit: "fix: resolve merge conflicts with main (..." | Re-trigger Greptile}

[greptile-apps]

The comment says "dir → parent-dir contains edges" but the edge inserted is parent_id → child_id (i.e., parent contains child). The variable names parentRow / childRow make the intended direction clear, but the comment points the wrong way and could mislead a future reader tracing the containment graph.

Suggested change

	// Wire dir -> parent-dir contains edges for the chain.
	for (const dir of affectedDirs) {
	// Wire parent-dir -> child-dir contains edges for the chain.
	for (const dir of affectedDirs) {

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 — comment now reads "Wire parent-dir -> child-dir contains edges for the chain.", matching the actual parentRow.id -> childRow.id insert.

[greptile-apps]

neighborFiles includes intra-directory edges

Neither the first half (n1.file >= @lo … n1.file < @hi, returns n2.file) nor the second half (returns n1.file) of the UNION restricts the other file to be outside the queried directory. A pair of files that both live inside dir but import each other would have each file appear as a "neighbour" of the other. getAncestorDirs on those intra-dir paths produces ancestors that are already in affectedDirs, so correctness is unaffected (the Set deduplicates). The same query pattern exists in the Rust find_neighbor_files. Worth noting as a latent source of minor extra work for repos with many intra-package cross-file imports, though the real cost is bounded and likely negligible in practice.

[carlos-alm]

Good catch — fixed rather than left as a note, since it's the same function I was already touching for the perf fix. Added NOT (other-side range) to both halves of the UNION so intra-directory pairs no longer surface as cross-directory neighbours at all, in both engines (TS neighborFiles and Rust find_neighbor_files).

[carlos-alm]

@greptileai