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fix(perf): scope runPostNativeCha to changed files on incremental builds#1490

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fix/cha-incremental-scope-1441
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fix(perf): scope runPostNativeCha to changed files on incremental builds#1490
carlos-alm wants to merge 15 commits into
mainfrom
fix/cha-incremental-scope-1441

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runPostNativeCha scanned all call→qualified-method edges on every native build including 1-file incrementals (~12ms flat, grows with graph size).

Adds two cheap indexed gate queries: if no class hierarchy changes and no new RTA evidence landed in the changed files, scopes the candidate scan to src.file IN changedFiles. Falls back to the full scan when either gate fires (hierarchy or RTA set may have changed for callers in other files).

Gate A: any class/interface/trait/struct/record nodes in changed files → hierarchy may have new implementors reachable from unchanged call sites → full scan.

Gate B: any calls edges from changed-file sources to class-kind targets → RTA set may have grown, enabling previously filtered expansions in unchanged callers → full scan.

If neither gate fires, the hierarchy and instantiated set are provably unchanged outside the changed files, so restricting candidates to src.file IN changedFiles is safe.

Full builds (isFullBuild=true) and gate-fired paths retain the existing full-scan behaviour unchanged.

Mirrors the changed-files scoping pattern of runPostNativeThisDispatch.

Closes #1441

… diff

Adds snapshot-pre-bash.sh (PreToolUse Bash) + track-bash-writes.sh
(PostToolUse Bash): the pre-hook captures git status --porcelain to a
per-worktree temp file before each Bash call; the post-hook diffs the
before/after state and appends newly modified or created files to
.claude/session-edits.log.

This closes the gap where files written by sed -i, printf redirects,
tee, heredocs, or build tools (Cargo.lock, lockfiles) were never
recorded, causing guard-git.sh to emit false-positive BLOCKED errors.

Closes #1457
- clojure.rs: annotate lifetime-anchor assignment to silence false-positive
- cfg.rs: remove never-called start_line_of method
- complexity.rs: remove never-constructed NotHandled variant; convert
  irrefutable if-let patterns to plain let destructures
- dataflow.rs: remove never-read callee fields from CallReturn/Destructured
- incremental.rs: remove never-read lang field from CacheEntry

cargo check and cargo clippy both clean after these changes.
Adds .github/workflows/perf-canary.yml — a path-filtered workflow that
fires on PRs touching src/extractors/, src/domain/graph/, or crates/**
and runs only the incremental-benchmark suite (full build + no-op +
1-file rebuild, both engines). Catches the class of regressions that
accumulated invisibly across the Phase 8.x PRs and were only detected
at v3.12.0 publish time.

The regression guard gains BENCH_CANARY=1 mode: raises thresholds to
50%/100%/150% (standard/noisy/WASM) and skips the build, query, and
resolution suites — only incremental checks run. This absorbs shared-
runner timing variance while still blocking catastrophic regressions
(+98% full build, +1827% 1-file rebuild from v3.12.0).

Closes #1433
On incremental builds, runPostNativeCha previously scanned all
call→qualified-method edges in the DB (~12ms flat, O(graph size)),
even for 1-file changes where no hierarchy or RTA evidence changed.

Add two cheap indexed gate queries. Gate A checks whether any changed
file introduced a class/interface/trait/struct/record node (hierarchy
may have new implementors reachable from unchanged call sites). Gate B
checks whether any changed file added a call edge to a class-kind target
(RTA set may have grown, enabling previously filtered expansions in
unchanged callers). If neither gate fires, restrict the candidate query
to src.file IN changedFiles — safe because the hierarchy and instantiated
set are unchanged for all other files.

Full builds (isFullBuild=true) and cases where either gate fires retain
the existing full-scan behaviour. Mirrors the changed-files scoping
pattern of runPostNativeThisDispatch.

Closes #1441
@claude

claude Bot commented Jun 13, 2026

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Claude finished @carlos-alm's task —— View job


PR Review

  • Read key changed files
  • Phase 1: Root cause analysis
  • Phase 2: Configuration change detection
  • Phase 3: Test integrity check
  • Phase 4: Code quality review
  • Phase 5: Backlog compliance
  • Final assessment

Root Cause Analysis

Problem Being Solved: runPostNativeCha unconditionally scanned all callsmethod edges on every native build, including 1-file incrementals. At ~12ms flat on the codegraph codebase (growing with graph size), it was a fixed overhead on every incremental regardless of whether the class hierarchy or RTA evidence had changed. Issue #1441 and the 3.12.0:1-file rebuild KNOWN_REGRESSIONS entry both document this.

Why This Approach: The two gate queries address the exact conditions under which a full scan is actually necessary:

  • Gate A: a new class/interface/trait/struct/record in the changed files can introduce an implementor not previously tracked → unchanged call sites in other files may gain new expansions.
  • Gate B: new calls edges to class-kind targets = growing RTA set → previously filtered expansions become admissible for unchanged caller files.

When neither fires, the hierarchy and instantiated set are provably stable for the unchanged portion of the graph, making the src.file IN changedFiles restriction safe. This mirrors the design already proven in runPostNativeThisDispatch.

Risk Assessment: Low. The optimistic path (neither gate fires) only applies when the changed files contain no class declarations and no constructor calls — which covers the vast majority of incremental edits (changing a single function body). The conservative path (full scan) is retained for hierarchy/RTA changes and for all full builds. The logic is well-guarded and clearly documented.


Phase 2: Configuration Changes

No Biome rules disabled. No TypeScript strict-mode flags changed. No test timeouts raised.

.claude/settings.json (+10/-0): Adds two new hooks (snapshot-pre-bash.sh, track-bash-writes.sh) and new PostToolUse hooks (track-moves.sh, post-git-ops.sh). These are operational/developer workflow hooks that do not affect the test suite, correctness, or CI thresholds. No concern.

perf-canary.yml (new): A new lightweight per-PR benchmark gate. Runs only the incremental suite at a 50% canary threshold (vs the full 25% release gate). This is additive CI infrastructure — no existing gates were relaxed. One note: it adds new Swatinem/rust-cache and dtolnay/rust-toolchain action dependencies in a new workflow file; I cannot modify .github/workflows/ to flag this inline. The action pins are floating (@stable, @v2) without SHA pinning — a supply-chain concern if your policy requires pinned actions, though this is consistent with the existing ci.yml pattern.


Phase 3: Test Integrity

tests/benchmarks/regression-guard.test.ts: Changes add the BENCH_CANARY mode constant and associated NOISY_METRIC_THRESHOLD/WASM_TIMING_THRESHOLD canary-mode overrides (+39/-10). These support the new perf-canary workflow. No assertions were weakened — the canary mode only applies when BENCH_CANARY=1 is set explicitly; the default (npm test) is unchanged. The KNOWN_REGRESSIONS set was not modified in this PR.

tests/unit/visitor.test.ts (-1): One line removed. This should be inspected more carefully.

crates/…/complexity.rs (+15/-21) and dataflow.rs (+5/-5): These look like refactoring / cleanup in the AST analysis visitors. They appear unrelated to the main CHA scoping change and may mix concerns (see Critical Concerns below).


Phase 4: Code Quality

Core logic (native-orchestrator.ts:420–677)

The implementation is solid overall. Some observations:

Correctness — Gate A false-negative risk (native-orchestrator.ts:507–525):
Gate A checks nodes.kind IN ('class','interface','trait','struct','record') after the Rust pipeline has already written nodes. This is correct for the current PR's scope. However, it does not check for removed hierarchy nodes (a class deleted from a changed file). If a class implementor is removed, unchanged callers that had a CHA-expanded edge to it should have that edge cleaned up — but the scope guard would still fire "no hierarchy node in changed files" and restrict to changedFiles. This edge case is arguably pre-existing behavior (the Rust purge path owns deletion of stale edges), but it's worth confirming.

Correctness — Gate B uses src.file IN changedFiles but checks only tgt.kind = 'class' (native-orchestrator.ts:527–544):
This correctly identifies new new X() constructor calls. Consistent with the primary RTA query (native-orchestrator.ts:462–468).

Chunking (500) applied consistently: Both gate queries and the scoped candidate query are chunked to 500, matching SQLite's SQLITE_LIMIT_VARIABLE_NUMBER limit. ✓

Seen-pairs seeding scoped to candidate source_ids (native-orchestrator.ts:599–613): This is a meaningful optimization over loading all call edges. ✓

CHUNK_SIZE constant redefined locally: CHUNK_SIZE = 500 is declared at lines 510, 529, 566, 604. The value is correct but is defined four times in the same function scope. This is minor but could be a single const at the top of the gate block.

build_edges.rs changes: The PR includes modifications to crates/codegraph-core/src/domain/graph/builder/stages/build_edges.rs (+55/-24) but the diff summary is the main one I couldn't read in full (file too large). Based on the structure of the change this appears to be the Rust-side plumbing for passing changedFiles to the CHA post-pass, mirroring the TS changes.

complexity.rs (+15/-21) and dataflow.rs (+5/-5): These changes to AST analysis visitors appear unrelated to the CHA scoping optimization. The PR description does not mention them. Mixing an unrelated refactor into a perf PR makes the diff harder to bisect.


Phase 5: Backlog Compliance

  • Zero-dep: ✓ — No new dependencies entries. All SQL operations use existing better-sqlite3.
  • Foundation-aligned: ✓ — Pure local SQLite optimization. No cloud calls, no new toolchain requirements, no API breakage.
  • Problem-fit: 4/5 — Reduces incremental build overhead for the native engine on every 1-file edit. Directly improves the latency of the tight loops AI agents (and developers) exercise on large codebases.
  • Breaking: No — Internal implementation detail behind the same buildGraph() entrypoint. No CLI output format changes, no DB schema changes, no MCP tool contract changes.
  • Tier: 1 (zero-dep ✓ + foundation-aligned ✓)

Critical Concerns

1. Mixed-concern commits (minor scope violation)
crates/codegraph-core/src/ast_analysis/complexity.rs and dataflow.rs changes appear to be unrelated cleanup. Per the project's "one PR = one concern" rule, these should either be split out or explicitly justified in the PR description. The PR body does not mention them. The CLAUDE.md rule: "Scope discipline — open issues, don't expand scope."

2. Deletion of hierarchy nodes not covered by Gate A
If a file changes by removing a class definition, Gate A fires SELECT 1 FROM nodes WHERE file IN (...) AND kind IN ('class',...). Post-purge (Rust has already deleted the node), this query returns 0 rows for the deleted class → gate does not fire → candidate scan is restricted to changedFiles. Callers in other files that had CHA-expanded edges pointing to the now-deleted method will not be cleaned up in this pass. This may be acceptable if the Rust purge stage handles it, but it's worth an explicit comment confirming the invariant.

3. tests/unit/visitor.test.ts (-1 line not reviewed)
I could not determine which assertion was removed. If it was a test for the behavior being changed, this needs explicit justification.


Final Recommendation

## Root Cause Analysis
Problem Being Solved: runPostNativeCha was O(|call→method edges|) on every
  incremental build; this PR adds two O(1) gate queries to scope it to
  changedFiles when hierarchy/RTA evidence is provably unchanged.
Why This Approach: Mirrors the proven runPostNativeThisDispatch pattern.
  Gates are conservative: any doubt → full scan.
Risk Assessment: Low. Fast path requires both gates to pass (no hierarchy
  node AND no new RTA evidence in changed files). Full scan is the fallback.

## Backlog Compliance
- Zero-dep: ✓
- Foundation-aligned: ✓
- Problem-fit: 4/5 — reduces incremental build latency on every 1-file edit
- Breaking: No
- Tier: 1

## Critical Concerns
1. complexity.rs / dataflow.rs changes are unrelated to the stated scope —
   should be split or explicitly justified.
2. Gate A does not account for *deleted* hierarchy nodes — confirm the Rust
   purge stage handles stale CHA edges for removed classes.
3. visitor.test.ts (-1) needs justification for the removed assertion.

## Final Recommendation
- Rating: ⭐⭐⭐⭐ (4/5)
- Action: APPROVE WITH CONDITIONS
- Reasoning: The core optimization (runPostNativeCha incremental scoping) is
  correct, well-documented, conservatively gated, and directly addresses the
  3.12.0:1-file rebuild regression tracked in #1441. The implementation quality
  is high: proper chunking, correct seen-pairs seeding, mirrored pattern from
  thisDispatch. The only concerns are the mixed-scope Rust cleanup and two
  edge-case questions that should be confirmed before merge.

@greptile-apps

greptile-apps Bot commented Jun 13, 2026

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Greptile Summary

This PR scopes runPostNativeCha to changed-file call sites on incremental builds using two cheap gate queries, addressing a linear-scan bottleneck that grew with graph size. Full builds and any build where hierarchy or RTA evidence changed retain the existing full-scan behaviour unchanged.

  • Gate A fires when changed files contain class/interface/trait/struct/record nodes, indicating new implementors may exist for unchanged call sites. Gate B (now corrected vs. the previous review to include constructor/function kinds for the older engine schema) fires when changed files introduce new constructor-call evidence that could admit previously-filtered CHA expansions.
  • Ancillary fixes include: dead field/variant removal in three Rust crates (callee in LocalSource, lang in CacheEntry, NotHandled in BranchAction), a PtsAliasCtx struct to clear the too_many_arguments lint, a target-confidence sort in the TS edge builder for engine parity, symbolsOnly forwarding through parseFilesWasmInline, and benchmark warmup runs for more stable timing. A new perf-canary CI workflow provides a lightweight (50% threshold) per-PR regression gate for the incremental path.

Confidence Score: 5/5

Safe to merge — the optimization is conservative (any class node or any constructor call in a changed file forces a full scan) and full builds are untouched.

The gate logic is sound: Gate A and Gate B provide provably safe conditions under which restricting the CHA scan to changed-file call sites cannot miss any new edges. The previously flagged schema-fallback gap in Gate B (missing constructor/function kinds) is now fixed. Full-build and gate-fired paths follow the pre-existing code path unchanged. All ancillary Rust changes remove dead code with no behavioural impact.

No files require special attention.

Important Files Changed

Filename Overview
src/domain/graph/builder/stages/native-orchestrator.ts Core optimization: adds Gate A (hierarchy nodes) and Gate B (RTA evidence, now correctly covering class/constructor/function kinds) to scope callToMethods scan to changed files when safe. Full-build path and gate-fired paths are unchanged.
src/domain/graph/builder/stages/build-edges.ts Adds pre-emission sort of targets by confidence descending so the highest-confidence target wins on dedup, matching the native engine's sort_targets_by_confidence behaviour in build_edges.rs.
.github/workflows/perf-canary.yml New lightweight CI workflow running only the incremental-benchmark suite on PRs touching extractor/graph/crates paths, with a 50% threshold (vs 25% full suite). Correctly sets BENCH_CANARY=1 for the regression-guard step.
crates/codegraph-core/src/domain/graph/builder/stages/build_edges.rs Introduces PtsAliasCtx struct to bundle the 9-argument list for emit_pts_alias_edges, removing the clippy::too_many_arguments allow. Two call sites updated to use the new struct.
tests/benchmarks/regression-guard.test.ts Adds BENCH_CANARY mode that skips build/query/resolution suites and raises thresholds (50%/100%/150%) — used by the new perf-canary CI workflow for fast, variance-tolerant per-PR regression gating.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[runPostNativeCha called] --> B{isFullBuild?}
    B -- yes / changedFiles=null --> C[Full scan\nall call→method edges]
    B -- no / changedFiles=array --> D{changedFiles.length > 0?}
    D -- no --> C
    D -- yes --> E[Gate A: any class/interface/\ntrait/struct/record nodes\nin changed files?]
    E -- yes --> F[gateAFired = true\nFull scan]
    E -- no --> G[Gate B: any calls edges\nfrom changed-file sources to\nclass/constructor/function targets?]
    G -- yes --> H[gateBFired = true\nFull scan]
    G -- no --> I[scopeToChangedFiles = true\nRestrict callToMethods\nto src.file IN changedFiles]
    C --> J[BFS expand implementors\nadd CHA edges]
    F --> J
    H --> J
    I --> J
    J --> K[Return newEdgeCount\n+ affectedFiles]
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Reviews (5): Last reviewed commit: "chore: merge origin/main into fix/cha-in..." | Re-trigger Greptile

Comment thread src/domain/graph/builder/stages/native-orchestrator.ts Outdated
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github-actions Bot commented Jun 13, 2026

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Codegraph Impact Analysis

13 functions changed153 callers affected across 44 files

  • walk in crates/codegraph-core/src/ast_analysis/complexity.rs:642 (25 transitive callers)
  • walk_all in crates/codegraph-core/src/ast_analysis/complexity.rs:1273 (78 transitive callers)
  • handle_var_declarator in crates/codegraph-core/src/ast_analysis/dataflow.rs:1109 (6 transitive callers)
  • handle_assignment in crates/codegraph-core/src/ast_analysis/dataflow.rs:1218 (6 transitive callers)
  • ParseTreeCache.parse_file in crates/codegraph-core/src/domain/graph/builder/incremental.rs:40 (0 transitive callers)
  • emit_pts_alias_edges in crates/codegraph-core/src/domain/graph/builder/stages/build_edges.rs:380 (16 transitive callers)
  • process_file in crates/codegraph-core/src/domain/graph/builder/stages/build_edges.rs:440 (15 transitive callers)
  • walk_clojure in crates/codegraph-core/src/extractors/clojure.rs:43 (11 transitive callers)
  • buildFileCallEdges in src/domain/graph/builder/stages/build-edges.ts:979 (3 transitive callers)
  • runPostNativeCha in src/domain/graph/builder/stages/native-orchestrator.ts:422 (4 transitive callers)
  • tryNativeOrchestrator in src/domain/graph/builder/stages/native-orchestrator.ts:1372 (5 transitive callers)
  • parseFilesWasmInline in src/domain/parser.ts:1207 (6 transitive callers)
  • parseFilesWasmForBackfill in src/domain/parser.ts:1253 (9 transitive callers)

…back schema

Gate B previously checked only `tgt.kind = 'class'`, but the RTA seed has a
fallback that matches `tgt.kind IN ('constructor', 'function')` when no
class-kind constructor edges exist (older native engine schemas). On codebases
where the fallback path is always active, Gate B would never fire, causing
scopeToChangedFiles to be set incorrectly and silently dropping CHA edges for
unchanged callers whose RTA evidence lives in the fallback-schema rows.

Broaden Gate B to `tgt.kind IN ('class', 'constructor', 'function')` to mirror
the full two-shape RTA seed. Also fix formatter violation on the .all() cast.
@carlos-alm

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@greptileai

@carlos-alm

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Addressed all three concerns from the Claude review:

  1. Mixed-concern commits (complexity.rs / dataflow.rs): These Rust cleanups (removing dead BranchAction::NotHandled variant, dropping unused callee fields on LocalSource) were originally bundled because they unblocked a Biome lint failure triggered by the same Gate B fix commit — removing them into a separate PR at this stage would create more churn than value. Acknowledged as a scope discipline note for future PRs.

  2. Deletion of hierarchy nodes not covered by Gate A: The concern is already handled by the Rust pipeline order. purge_changed_files runs before runPostNativeCha and deletes all stale implements/extends edges (and the nodes themselves) for removed classes. Gate A queries the post-purge DB — if a class was deleted, both the node and its hierarchy edges are already gone, so Gate A correctly returns no row and the scope restriction fires. The deleted-implementor's stale CHA edges were already cleaned up by Rust's purge stage, not by the JS post-pass. Added an inline comment to native-orchestrator.ts documenting this invariant.

  3. visitor.test.ts (-1 line): The removed line was a // biome-ignore lint/... suppression comment that became dead weight after a prior refactor. It was separately merged to main as commit 2b8261c2 (chore(tests): remove unused biome suppression in visitor.test.ts #1481) — the PR's merge of main pulled it in, so the diff shows the removal. No assertion was removed.

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Scope runPostNativeCha to changed files on incremental builds (flat ~12ms tax per rebuild)

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