fix: align Java interface dispatch across wasm/native/hybrid (#1503)

* chore: gitignore napi-generated artifacts in crates/codegraph-core

* chore(tests): remove unused biome suppression in visitor.test.ts

* fix(titan-run): sync --start-from enum and phase-timestamp list with actual phases

* fix(hooks): track Bash file modifications via before/after git status 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

* chore(native): remove dead code (unused var, method, variant, fields)

- 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.

* refactor(native): extract emit_pts_alias_edges params into PtsAliasCtx struct

* fix(wasm): sort call targets by confidence before emit to match native engine

* fix(bench): add 2 warmup runs and raise INCREMENTAL_RUNS to 5 for incremental tiers

* ci(bench): add per-PR perf canary for extractor/graph/native 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

* fix(perf): plumb symbolsOnly through parseFilesWasmInline to skip analysis visitors

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

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

* fix(native): add post-pass phase timings to result.phases

Times each JS post-pass in tryNativeOrchestrator and exposes the
measurements in BuildResult.phases:

- gapDetectMs  — dropped-language gap detection + backfill
- chaMs        — CHA expansion (interface dispatch)
- thisDispatchMs — this/super dispatch WASM re-parse (was already
                   tracked but now properly named alongside the rest)
- reclassifyMs — scoped role re-classification after edge insertion
- techniqueBackfillMs — technique-column UPDATE on native-written edges

Previously only thisDispatchMs was reported, causing wall-clock vs
phaseSum to diverge by 1.1s+ on 1-file rebuilds and making benchmark
regressions undiagnosable from committed history.

Updates update-incremental-report.ts to render the new phases in a
collapsible details block under each engine's 1-file rebuild section.

Closes #1434

* fix(perf): correct INLINE_BACKFILL_THRESHOLD docstring; raise threshold for required-tier grammars

The docstring claimed pool cost was "amortised over enough parse work" —
measurements show IPC overhead scales linearly (~55–64ms/file pool vs
~8–10ms/file inline). The real motivation is crash safety for exotic WASM
grammars (#965); JS/TS/TSX (required-tier, used in all this-dispatch
backfill calls) have never triggered the V8 fatal crash class and are safe
to run inline.

Raise threshold 16 → 32 to keep typical this-dispatch batches (≤ 18 files
on the codegraph corpus) on the inline fast path. Exotic-language drops are
almost always well under 32 files and also benefit from the inline path
without meaningful crash risk increase.

Closes #1435

* fix(perf): guard post-native passes against unnecessary work on 1-file incremental rebuilds

On 1-file native incremental builds, two JS post-passes ran unconditionally
even when they had no work to do:

- `backfillNativeDroppedFiles`: called whenever changedCount > 0, even when
  detectDroppedLanguageGap returned an empty gap. Gate now checks
  gap.missingAbs.length > 0 || gap.staleRel.length > 0 directly, matching
  backfillNativeDroppedFiles's own internal early-exit guard.

- Node/edge COUNT(*) re-count: ran unconditionally after all post-passes even
  when none of them wrote any edges. COUNT(*) over 50K+ edge tables is
  non-trivial, especially via the NativeDbProxy napi-rs round-trip. Now gated
  on postPassWroteData (backfill | CHA edges | this-dispatch edges).

Closes #1454

* chore(types): remove dead protoMethodsMs field and stale comment

The post-pass it timed (runPostNativePrototypeMethods) was deleted in
b5c03a2 when func-prop extraction moved to Rust (#1432). The optional
field was never set by any code path that survived the deletion.

Also remove the stale reference to "prototype-methods post-pass" from
the parseFilesWasmForBackfill docstring — only the this-dispatch
post-pass uses symbolsOnly now.

Closes #1432

* fix: class-scope field annotation typeMap keys to prevent cross-class collision

Field type annotations (`private repo: OrderRepository`) were seeded as bare
file-wide typeMap keys, causing `this.repo` inside `UserService` to resolve to
`OrderRepository` when both classes had a `repo` field (issue #1458).

Both extractors (TS `handleFieldDefTypeMap` and Rust `field_definition` branch)
now seed `ClassName.field` keys at confidence 0.9, matching the `CallerClass.X`
resolver fallback added in PR #1382. Bare keys are kept at confidence 0.6 as
fallbacks for single-class files or class expressions where no enclosing class
name is available.

Both engines change identically — parity preserved.

* fix(bench): update elixir/julia/objc expected-edges to module-qualified names

The resolution benchmark uses WASM-built graphs where the Elixir, Julia,
and Objective-C extractors emit module-qualified symbol names (Main.run,
App.main, UserService.create_user, etc.). The expected-edges manifests
were written with bare unqualified names (run, main, create_user), so
every correctly-resolved edge appeared as a false positive and every
expected edge appeared as a false negative — causing all three languages
to show 0% precision even though resolution was working correctly.

Root cause: starting in v3.12.0, cross-module call resolution began working
for these languages (via the improved receiver-dispatch and same-class
fallback in resolveByMethodOrGlobal / build-edges.ts). With 0 edges
previously resolved, the name mismatch was invisible; once edges started
resolving, the manifests showed 17 FP (elixir), 11 FP (julia), 6 FP
(objc) — all correctly resolved edges misidentified as false positives.

Fix:
- Update all three expected-edges.json manifests to use the
  module-qualified names matching actual extractor output:
  elixir: Main.run, UserService.create_user, Validators.validate_user, etc.
  julia:  App.main, Service.create_user, Repository.new_repo, etc.
  objc:   full ObjC selectors (createUserWithId:name:email:, isValidEmail:, etc.)
          plus add main -> run (plain C call correctly resolved)
- Ratchet THRESHOLDS for all three:
  elixir: precision 0.0 -> 1.0, recall 0.0 -> 0.8  (17/21 resolved)
  julia:  precision 0.0 -> 1.0, recall 0.0 -> 0.7  (11/15 resolved)
  objc:   precision 0.0 -> 1.0, recall 0.0 -> 0.4   (6/13 resolved)

Remaining FNs are genuine unresolved edges (same-file bare calls in
elixir/julia, receiver-typed message sends in objc) — not regressions.

Closes #1447

* fix(wasm): emit receiver edges for declaration-typed locals in C++/CUDA

The JS C++ and CUDA extractors had no handler for 'declaration' AST nodes,
so typeMap was never seeded for statically-typed locals (e.g. 'UserService svc;').
Without a typeMap entry for 'svc', resolveReceiverEdge had nothing to look up and
silently skipped the receiver edge.

Add handleCppDeclaration / handleCudaDeclaration to both extractors. They mirror
match_c_family_type_map ('declaration' branch) from the native Rust path: extract
the type node text and seed typeMap[varName] = { type, confidence: 0.9 } for each
identifier or init_declarator child. Primitive types (int, char, bool, …) are
skipped to avoid spurious edges.

parity-compare.mjs --langs cpp,cuda --hybrid: PARITY OK (wasm = native = hybrid)
All 3044 tests pass.

* fix(native): resolve Go factory and Python constructor receiver types in Rust solver

Go extractor was only seeding typeMap for var_spec and parameter_declaration,
missing short_var_declaration. Added infer_short_var_types to handle:
- x := Struct{} → conf 1.0 (composite literal)
- x := &Struct{} → conf 1.0 (address-of composite)
- x := NewFoo() / x := pkg.NewFoo() → conf 0.7 (New* factory prefix)

Python extractor was only seeding typeMap for typed_parameter and
typed_default_parameter, missing plain assignment. Added
infer_py_assignment_type to handle:
- order = Order(...) → conf 1.0 (uppercase constructor)
- obj = Module.Class(...) → conf 0.7 (uppercase module prefix, non-builtin)

Both mirror the existing JS extractors exactly. Parity check for
go and python: wasm vs native/hybrid OK.

* fix: align enclosing-caller attribution for variable bindings (haskell, zig)

Both engines used different rules for attributing calls inside variable bindings:

WASM: attributed to the narrowest enclosing span regardless of kind, so
local variable declarations inside fn main() shadowed the enclosing function
(Zig: calls attributed to repo/svc variables instead of main), and nested
let-bindings inside a Haskell do-block shadowed the top-level main binding.

Native: loaded allNodes from a query that excluded 'variable' kind, so
top-level Haskell bind nodes (main = do …, kind='variable') never matched
in defs_with_ids, causing all calls to fall back to the file node.

Unified rule implemented in findCaller (TS) and find_enclosing_caller (Rust):
- Function/method definitions are preferred over any variable/constant binding
  as the enclosing caller scope — local var declarations inside a function
  body never shadow the enclosing function (fixes Zig repo/svc attribution).
- When no function/method encloses the call, fall back to the WIDEST
  (outermost) variable/constant binding — this handles Haskell where main
  is a top-level bind node with kind 'variable'. Widest span is used so that
  nested let-bindings do not shadow the outer main binding.
- File node remains the absolute last resort.

Also adds 'variable' to NODE_KIND_FILTER_SQL (JS) and EDGE_NODE_KIND_FILTER
(Rust pipeline.rs) so top-level variable bindings are included in the allNodes
set available for caller matching.

parity-compare.mjs --langs haskell,zig --hybrid: PARITY OK — 2/2 fixtures.

* chore(lint): fix unused import and formatting in cpp/cuda extractors and test

Remove unused TypeMapEntry import from cpp.ts and cuda.ts, reformat
primitive-type Set literals and test expect() calls to satisfy biome
line-length rules.

* fix: align Java interface dispatch across wasm/native/hybrid

Java was the only fixture where all three build paths (wasm, native,
hybrid) disagreed pairwise.

Bug 1 — WASM typeMap pollution:
`handleJavaLocalVarDecl` used last-wins Map.set(), so the local
`InMemoryUserRepository repo` in the static `createDefault()` method
silently overrode the constructor parameter `UserRepository repo`.
This caused WASM to bypass the interface and resolve directly to the
concrete class, producing no interface edge and the wrong receiver.
Fix: switch to first-wins `setTypeMapEntry` to match Rust extractor
semantics. First-wins preserves the interface annotation that drives
correct CHA dispatch.

Bug 2 — native vs wasm/hybrid confidence mismatch:
`runPostNativeCha` (native orchestrator path) used
`computeConfidence − CHA_DISPATCH_PENALTY = 0.7 − 0.1 = 0.6`,
while `runChaPostPass` (DB post-pass used by wasm and hybrid) hardcodes
0.8. Fix: align `runPostNativeCha` to also use 0.8.

Result: all three build paths now emit identical edges and confidences.
`parity-compare.mjs --langs java --hybrid` passes.
Updated expected-edges.json to include both the interface declaration
edge (TypeRepository.X at 0.7) and the CHA-expanded impl edge
(InMemoryUserRepository.X at 0.8), which are the correct semantics for
an interface-typed receiver.

Closes #1469

* fix: use setTypeMapEntry in cpp/cuda extractors and extract CHA_DISPATCH_CONFIDENCE constant

Switch handleCppDeclaration and handleCudaDeclaration from last-wins
ctx.typeMap.set() to first-wins setTypeMapEntry(), fixing the same flat
typeMap pollution bug this PR corrects in java.ts.

Extract the CHA dispatch confidence value to a named CHA_DISPATCH_CONFIDENCE
constant in helpers.ts so runChaPostPass and the native orchestrator share
a single source of truth instead of two synchronized magic numbers.

* fix(native): extend Gate B RTA check to cover constructor/function kinds (#1503)

The incremental scoping gate in runPostNativeCha only checked tgt.kind = 'class'
for new RTA evidence, but the adjacent two-tier RTA collection also falls back to
constructor/function kinds for databases written by older native engine versions.
On such incremental builds Gate B would never fire, causing the scan to be wrongly
scoped to changed files and missing CHA expansion for unchanged-file call sites.

Author: carlos-alm

src/domain/graph/builder/helpers.ts

@@ -361,6 +361,9 @@ export function batchInsertEdges(db: BetterSqlite3Database, rows: unknown[][]):
   }
 }
 
+/** Confidence assigned to CHA-expanded interface/abstract dispatch edges. */
+export const CHA_DISPATCH_CONFIDENCE = 0.8;
+
 /**
  * CHA (Class Hierarchy Analysis) post-pass.
  *
@@ -514,7 +517,7 @@ export function runChaPostPass(db: BetterSqlite3Database): number {
             const key = `${source_id}|${methodNode.id}`;
             if (seen.has(key)) continue;
             seen.add(key);
-            newEdges.push([source_id, methodNode.id, 'calls', 0.8, 0, 'cha']);
+            newEdges.push([source_id, methodNode.id, 'calls', CHA_DISPATCH_CONFIDENCE, 0, 'cha']);
           }
         }
 

src/domain/graph/builder/stages/native-orchestrator.ts

@@ -49,6 +49,7 @@ import type { PipelineContext } from '../context.js';
 import {
   batchInsertEdges,
   batchInsertNodes,
+  CHA_DISPATCH_CONFIDENCE,
   collectFiles as collectFilesUtil,
   fileHash,
   fileStat,
@@ -570,8 +571,8 @@ function runPostNativeCha(
   }
 
   // Find existing call edges targeting qualified methods (e.g., 'IWorker.doWork').
-  // Include the caller node's file so confidence can be computed file-pair-aware,
-  // matching the WASM path's computeConfidence(callerFile, targetFile, null) - CHA_DISPATCH_PENALTY formula.
+  // Include caller_file and method_file so affectedFiles can be populated for
+  // incremental role reclassification; confidence is CHA_DISPATCH_CONFIDENCE matching runChaPostPass.
   // When scopeToChangedFiles is true, restrict to call sites in the changed files
   // (safe because no hierarchy or RTA evidence changed outside those files).
   let callToMethods: Array<{ source_id: number; method_name: string; caller_file: string | null }>;
@@ -667,10 +668,7 @@ function runPostNativeCha(
             const key = `${source_id}|${methodNode.id}`;
             if (seen.has(key)) continue;
             seen.add(key);
-            // Use the same hardcoded 0.8 that runChaPostPass (helpers.ts) uses for
-            // DB-level CHA dispatch edges. This aligns the native orchestrator path
-            // with the WASM and hybrid paths, which both go through runChaPostPass.
-            const conf = 0.8;
+            const conf = CHA_DISPATCH_CONFIDENCE;
             newEdges.push([source_id, methodNode.id, 'calls', conf, 0, 'cha']);
             newEdgeCount++;
             if (caller_file) affectedFiles.add(caller_file);

src/extractors/cpp.ts

@@ -5,7 +5,7 @@ import type {
   TreeSitterNode,
   TreeSitterTree,
 } from '../types.js';
-import { extractModifierVisibility, findChild, nodeEndLine } from './helpers.js';
+import { extractModifierVisibility, findChild, nodeEndLine, setTypeMapEntry } from './helpers.js';
 
 /**
  * Extract symbols from C++ files.
@@ -236,7 +236,7 @@ function handleCppDeclaration(node: TreeSitterNode, ctx: ExtractorOutput): void
     if (!nameNode) continue;
     const varName = unwrapCppDeclaratorName(nameNode);
     if (varName) {
-      ctx.typeMap.set(varName, { type: typeName, confidence: 0.9 });
+      setTypeMapEntry(ctx.typeMap, varName, typeName, 0.9);
     }
   }
 }

src/extractors/cuda.ts

@@ -5,7 +5,7 @@ import type {
   TreeSitterNode,
   TreeSitterTree,
 } from '../types.js';
-import { extractModifierVisibility, findChild, nodeEndLine } from './helpers.js';
+import { extractModifierVisibility, findChild, nodeEndLine, setTypeMapEntry } from './helpers.js';
 
 /**
  * Extract symbols from CUDA files.
@@ -236,7 +236,7 @@ function handleCudaDeclaration(node: TreeSitterNode, ctx: ExtractorOutput): void
     if (!nameNode) continue;
     const varName = extractCudaFieldName(nameNode);
     if (varName) {
-      ctx.typeMap.set(varName, { type: typeName, confidence: 0.9 });
+      setTypeMapEntry(ctx.typeMap, varName, typeName, 0.9);
     }
   }
 }