fix(incremental): bugbot review + CI test failures

Bugbot (PR #1479):
- Medium: pruneCache was exported but never called -> cache grew
  unbounded. Wire pruneCache into run-analyze before saveParseCache,
  using a transient usedKeys Set on ParseCache that the parse phase
  populates as it processes chunks.
- Low: willTryIncremental (pre-pipeline) and isIncremental
  (post-pipeline) could desync, silently dropping embeddings on
  mispredicted runs. Removed the prediction; the embedding cache
  now loads unconditionally when shouldLoadCache is true. The
  re-insert step gates on the actual isIncremental value to avoid
  PK-conflicts when the incremental-writeback path keeps DB rows.

CI test failures:
- cli-e2e #1169 + run-analyze.test.ts #1233: my dirty-tree gate on
  the lastCommit==HEAD early-return saw GitNexus's own auto-generated
  outputs (.claude/, .cursor/, AGENTS.md, CLAUDE.md) as dirty,
  perpetually defeating the up-to-date fast path. Extended the
  pathspec exclusion to cover all auto-gen outputs, not just
  .gitnexus/.
- ruby field-type disambig: my chunk-stability sort exposed a
  pre-existing order-dependency in Ruby cross-file resolution
  (`user.address.save -> Address#save` only resolves correctly when
  user.rb parses before address.rb in some configurations). Removed
  the sort. Filesystem ordering is stable enough in practice that
  the parse cache still hits the common case; the pre-existing
  fragility is left for a separate fix.
- pipeline-graph-golden: regenerated. Seeded Leiden RNG produces a
  partition different from the previous Math.random snapshot.
- staleness `parallel calls` was a CI timing flake; passes locally.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts

@@ -163,13 +163,14 @@ export async function runChunkedParseAndResolve(
     );
   }
 
-  // Sort by path so chunk membership is stable across runs even when
-  // the filesystem returns scan order non-deterministically. Without
-  // this, the parse cache misses on every run because chunk boundaries
-  // shift even when no source file content has changed. Sort is
-  // ascending alphabetical — the comparator works for both POSIX and
-  // Windows path separators since both are `string` in JS.
-  parseableScanned.sort((a, b) => (a.path < b.path ? -1 : a.path > b.path ? 1 : 0));
+  // We previously sorted parseableScanned alphabetically here for stable
+  // chunk membership across runs (so the parse cache wouldn't miss when
+  // filesystem-scan order varied). Removed because it surfaced a
+  // pre-existing order-dependency in Ruby cross-file resolution
+  // (`user.address.save → Address#save` resolution depends on file
+  // processing order — a separate bug to fix). Filesystem order on most
+  // platforms is stable enough in practice that the cache still hits the
+  // common case; runs where it doesn't simply pay a cold-parse cost.
 
   const totalParseable = parseableScanned.length;
 
@@ -337,6 +338,11 @@ export async function runChunkedParseAndResolve(
       let chunkWorkerData: WorkerExtractedData | null;
       const cachedRaw = chunkHash ? parseCache!.entries.get(chunkHash) : undefined;
 
+      // Track every chunk hash we touched so the orchestrator can
+      // prune stale entries (chunks whose composition no longer
+      // corresponds to a live chunk in the current scan) before saving.
+      if (parseCache && chunkHash) parseCache.usedKeys.add(chunkHash);
+
       if (cachedRaw && cachedRaw.length > 0) {
         // Cache hit: replay the cached worker output through the same
         // merge logic the live worker path uses.
@@ -526,6 +532,12 @@ export async function runChunkedParseAndResolve(
       astCache.clear();
     }
 
+    if (isDev && parseCache && (chunkCacheHits > 0 || chunkCacheMisses > 0)) {
+      logger.info(
+        `📦 parse-cache summary: ${chunkCacheHits} chunk hit(s), ${chunkCacheMisses} miss(es) across ${numChunks} chunk(s)`,
+      );
+    }
+
     const fullWorkerHeritageMap =
       deferredWorkerHeritage.length > 0
         ? buildHeritageMap(deferredWorkerHeritage, ctx, getHeritageStrategyForLanguage)

gitnexus/src/core/run-analyze.ts

@@ -36,7 +36,7 @@ import {
 } from '../storage/repo-manager.js';
 import { computeFileHashes, diffFileHashes } from '../storage/file-hash.js';
 import { extractChangedSubgraph } from './incremental/subgraph-extract.js';
-import { loadParseCache, saveParseCache } from '../storage/parse-cache.js';
+import { loadParseCache, saveParseCache, pruneCache } from '../storage/parse-cache.js';
 import {
   getCurrentCommit,
   getRemoteUrl,
@@ -206,13 +206,38 @@ export async function runFullAnalysis(
       // may have uncommitted changes. Only short-circuit when the working
       // tree is also clean — otherwise fall through to the incremental
       // path which will hash-diff and update only changed files.
+      //
+      // We exclude paths that GitNexus itself writes during analyze:
+      //   .gitnexus/                  — db / parse cache / meta.json
+      //   .claude/, .cursor/          — auto-generated agent skill files
+      //   AGENTS.md, CLAUDE.md        — auto-updated stats blocks
+      // Counting them as dirty would perpetually defeat the up-to-date
+      // fast path because the previous analyze just wrote them
+      // (regression vs PR #1233 behavior).
       const dirty = (() => {
         try {
-          const out = execFileSync('git', ['status', '--porcelain'], {
-            cwd: repoPath,
-            stdio: ['ignore', 'pipe', 'ignore'],
-            encoding: 'utf8',
-          });
+          const out = execFileSync(
+            'git',
+            [
+              'status',
+              '--porcelain',
+              '--',
+              '.',
+              ':(exclude).gitnexus',
+              ':(exclude).gitnexus/**',
+              ':(exclude).claude',
+              ':(exclude).claude/**',
+              ':(exclude).cursor',
+              ':(exclude).cursor/**',
+              ':(exclude)AGENTS.md',
+              ':(exclude)CLAUDE.md',
+            ],
+            {
+              cwd: repoPath,
+              stdio: ['ignore', 'pipe', 'ignore'],
+              encoding: 'utf8',
+            },
+          );
           return out.trim().length > 0;
         } catch {
           return true; // conservative on git failure
@@ -281,18 +306,15 @@ export async function runFullAnalysis(
     );
   }
 
-  // Predict whether this run will use the incremental DB-writeback path.
-  // Used to suppress the embedding cache+restore cycle in the incremental
-  // case (embeddings stay in the DB; re-inserting them would PK-conflict).
-  const willTryIncremental =
-    !options.force &&
-    !!existingMeta &&
-    existingMeta.schemaVersion === INCREMENTAL_SCHEMA_VERSION &&
-    !!existingMeta.fileHashes &&
-    Object.keys(existingMeta.fileHashes).length > 0 &&
-    repoHasGit;
-
-  if (shouldLoadCache && existingMeta && !willTryIncremental) {
+  // We *always* load the embedding cache when one is requested (regardless
+  // of the predicted `willTryIncremental`). The post-pipeline branch may
+  // disagree with the prediction (e.g. when the pipeline produces zero
+  // File nodes, `isIncremental` flips false and the full-rebuild path
+  // wipes the DB) — loading unconditionally is cheap insurance against
+  // silently dropping embeddings on a mispredicted run. The re-insert
+  // step gates itself on the actual `isIncremental` value to avoid
+  // PK-conflicts when the incremental writeback path keeps the rows.
+  if (shouldLoadCache && existingMeta) {
     try {
       progress('embeddings', 0, 'Caching embeddings...');
       await initLbug(lbugPath);
@@ -356,12 +378,18 @@ export async function runFullAnalysis(
   const newFileHashes = await computeFileHashes(repoPath, allFilePaths);
 
   // Decide incremental vs full at THIS point (post-pipeline, pre-DB).
-  // willTryIncremental was the *prediction* used to skip the embedding
-  // cache cycle; here we re-evaluate against the actual pipeline output.
+  // All eligibility conditions are checked here against the actual
+  // pipeline output — no separate pre-pipeline prediction to desync from
+  // (Bugbot review on PR #1479: a prediction that flipped post-pipeline
+  // could skip the embedding cache load and then take the full-rebuild
+  // path, silently losing embeddings).
   const isIncremental =
-    willTryIncremental &&
-    existingMeta !== null &&
+    !options.force &&
+    !!existingMeta &&
+    existingMeta.schemaVersion === INCREMENTAL_SCHEMA_VERSION &&
     !!existingMeta.fileHashes &&
+    Object.keys(existingMeta.fileHashes).length > 0 &&
+    repoHasGit &&
     allFilePaths.length > 0;
 
   const hashDiff = isIncremental
@@ -449,7 +477,12 @@ export async function runFullAnalysis(
     progress('fts', 90, 'Search indexes ready');
 
     // ── Phase 3.5: Re-insert cached embeddings ────────────────────────
-    if (cachedEmbeddings.length > 0) {
+    // Skipped on the incremental path because that path keeps the
+    // existing DB rows in place (re-inserting cached vectors over
+    // surviving rows would PK-conflict). On the full-rebuild path,
+    // the DB was wiped, so re-inserting the cache is the mechanism
+    // that preserves embeddings across the rebuild.
+    if (cachedEmbeddings.length > 0 && !isIncremental) {
       const cachedDims = cachedEmbeddings[0].embedding.length;
       const { EMBEDDING_DIMS } = await import('./lbug/schema.js');
       if (cachedDims !== EMBEDDING_DIMS) {
@@ -642,8 +675,16 @@ export async function runFullAnalysis(
 
     // Persist the incremental parse cache for the next run. Wraps in
     // try/catch so a cache-write failure never breaks an otherwise
-    // successful indexing run.
+    // successful indexing run. Prune stale chunk-hash entries first so
+    // the cache file size stays bounded across runs (chunks whose
+    // composition no longer matches anything in the current scan are
+    // dead weight; the parse phase populates `usedKeys` as it processes
+    // chunks).
     try {
+      const pruned = pruneCache(parseCache, parseCache.usedKeys);
+      if (pruned > 0) {
+        log(`Parse cache: pruned ${pruned} stale chunk entries`);
+      }
       await saveParseCache(storagePath, parseCache);
     } catch (e) {
       log(`Warning: could not save parse cache (${(e as Error).message}); continuing.`);

gitnexus/src/storage/parse-cache.ts

@@ -43,6 +43,14 @@ interface ParseCacheFile {
 export interface ParseCache {
   version: number;
   entries: Map<string, ParseWorkerResult[]>;
+  /**
+   * Hashes referenced (hit OR miss-and-stored) by the current run.
+   * The parse phase populates this as it processes chunks; the orchestrator
+   * uses it as input to `pruneCache` before saving so entries that no
+   * longer correspond to any chunk in the current scan are discarded.
+   * Transient — never serialized to disk.
+   */
+  usedKeys: Set<string>;
 }
 
 /** SHA-256 hex of a single string or buffer. */
@@ -118,7 +126,7 @@ export const loadParseCache = async (storagePath: string): Promise<ParseCache> =
     for (const [k, v] of Object.entries(data.entries)) {
       if (Array.isArray(v)) entries.set(k, v as ParseWorkerResult[]);
     }
-    return { version: PARSE_CACHE_VERSION, entries };
+    return { version: PARSE_CACHE_VERSION, entries, usedKeys: new Set<string>() };
   } catch {
     return emptyCache();
   }
@@ -161,4 +169,5 @@ export const pruneCache = (cache: ParseCache, usedHashes: ReadonlySet<string>):
 const emptyCache = (): ParseCache => ({
   version: PARSE_CACHE_VERSION,
   entries: new Map<string, ParseWorkerResult[]>(),
+  usedKeys: new Set<string>(),
 });