@specship/specship-darwin-arm64 0.28.0 → 0.30.0

package/lib/dist/enforce/enforce.js

@@ -51,6 +51,8 @@ var __importStar = (this && this.__importStar) || (function () {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ALL_CHECKS = exports.ENFORCE_CONFIG_FILE = void 0;
 exports.normalizePath = normalizePath;
+exports.undeclaredLinkFindings = undeclaredLinkFindings;
+exports.branchBrokenFindings = branchBrokenFindings;
 exports.evaluateEnforcement = evaluateEnforcement;
 exports.loadEnforceConfig = loadEnforceConfig;
 exports.strictEnforceConfig = strictEnforceConfig;
@@ -59,6 +61,7 @@ const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const maintainability_1 = require("../graph/maintainability");
 const suppressions_1 = require("./suppressions");
+const spec_link_resolver_1 = require("../resolution/spec-link-resolver");
 /**
  * Project-relative, forward-slashed, no `./` prefix. Link target paths, spec
  * source paths and git's output all have to compare in one shape before
@@ -67,6 +70,48 @@ const suppressions_1 = require("./suppressions");
 function normalizePath(p) {
     return p.replace(/\\/g, '/').replace(/^\.\//, '').replace(/^\/+/, '');
 }
+/**
+ * Provenances a fresh clone re-derives from the checked-out files: the spec
+ * file's `implementations:` / `verifies:` blocks and `@implements` /
+ * `@verifies` code comments.
+ */
+const DECLARED_PROVENANCES = new Set(['spec-declaration', 'code-comment']);
+function linkKey(l) {
+    // Canonical dotted qname (REQ-LINKFIX-002) so `Class.method` and
+    // `Class::method` rows count as one logical link.
+    return [l.specId, normalizePath(l.targetFilePath), (0, spec_link_resolver_1.canonicalQualifiedName)(l.targetQualifiedName), l.kind].join('\u0000');
+}
+/**
+ * Undeclared links (REQ-MULTIDEV-002.A1): an `agent-asserted` row with no
+ * declared twin — no `spec-declaration` or `code-comment` row for the same
+ * spec, target and kind. A fresh clone never sees it.
+ */
+function undeclaredLinkFindings(links) {
+    const declared = new Set(links.filter((l) => DECLARED_PROVENANCES.has(l.provenance)).map(linkKey));
+    const seen = new Set();
+    const findings = [];
+    for (const l of links) {
+        if (l.provenance !== 'agent-asserted')
+            continue;
+        const key = linkKey(l);
+        if (declared.has(key) || seen.has(key))
+            continue;
+        seen.add(key);
+        findings.push(`${l.specId} → ${l.targetFilePath}:${l.targetQualifiedName} — undeclared (${l.provenance}): ` +
+            'add it to implementations:/verifies: or an @implements comment');
+    }
+    return findings;
+}
+/**
+ * Branch-broken links (REQ-MULTIDEV-002.A2/A3): orphaned/broken now, but the
+ * target resolved at the ref — so this branch broke it. A link already
+ * unresolved at the ref is not reported.
+ */
+function branchBrokenFindings(entries) {
+    return entries
+        .filter((e) => e.resolvedAtRef)
+        .map((e) => `${e.link.specId} → ${e.link.targetFilePath}:${e.link.targetQualifiedName} — ${e.link.state} on this branch, resolved at ${e.ref}`);
+}
 function evaluateEnforcement(deps, config = {}, scope) {
     const gate = config.gate ?? {};
     const exclude = new Set(config.behaviour?.exclude ?? []);
@@ -190,6 +235,18 @@ function evaluateEnforcement(deps, config = {}, scope) {
             });
         }
     }
+    // --- undeclared links (REQ-MULTIDEV-002) ---
+    if (deps.links !== undefined) {
+        const findings = undeclaredLinkFindings(deps.links);
+        checks.push({ check: 'undeclaredLinks', gating: gate.undeclaredLinks === true, passed: findings.length === 0, findings });
+    }
+    // --- branch-broken links (REQ-MULTIDEV-002) — only for a `--since` run ---
+    if (deps.brokenAtRef !== undefined) {
+        const findings = branchBrokenFindings(deps.brokenAtRef);
+        checks.push({
+            check: 'branchBroken', gating: gate.branchBroken === true, passed: findings.length === 0, findings, scoped: true,
+        });
+    }
     const gatedFailures = checks.filter((c) => c.gating && !c.passed && !c.skipped).map((c) => c.check);
     return { checks, gatedFailures, passed: gatedFailures.length === 0 };
 }
@@ -212,13 +269,20 @@ function loadEnforceConfig(projectRoot) {
     return {};
 }
 /** All check names, for `--strict` / `--enable-gate` validation. */
-exports.ALL_CHECKS = ['drift', 'fitness', 'maintainability', 'behaviour', 'suppressions', 'mutation'];
+exports.ALL_CHECKS = [
+    'drift', 'fitness', 'maintainability', 'behaviour', 'suppressions', 'mutation', 'undeclaredLinks', 'branchBroken',
+];
 /**
  * The `--strict` override (REQ-ENFORCE-004.A2): every check gates for this
  * run only. Nothing is read from or written to the project config.
  */
 function strictEnforceConfig() {
-    return { gate: { drift: true, fitness: true, maintainability: true, behaviour: true, suppressions: true, mutation: true } };
+    return {
+        gate: {
+            drift: true, fitness: true, maintainability: true, behaviour: true, suppressions: true, mutation: true,
+            undeclaredLinks: true, branchBroken: true,
+        },
+    };
 }
 /**
  * Persist gating for the named checks into `specship.config.json`

package/lib/dist/enforce/enforce.js.map

@@ -1 +1 @@
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package/lib/dist/extraction/index.d.ts

@@ -7,6 +7,19 @@ import * as fs from 'fs';
 import { ExtractionResult, ExtractionError } from '../types';
 import { QueryBuilder } from '../db/queries';
 import { Ignore } from 'ignore';
+/**
+ * Version of the extractor's output. Bump it whenever an extraction fix
+ * changes what an UNCHANGED file produces (REQ-HTMLLEX-002): a stored index
+ * stamped with an older version is stale, and the next full sync / indexAll
+ * re-extracts every tracked file in {@link EXTRACTION_STALE_LANGUAGES} even
+ * though its content hash still matches.
+ *
+ * - 1 (implicit / missing): pre-HTMLLEX extraction.
+ * - 2: declarations survive `<!--` / `-->` inside JS/TS literals (HTMLLEX-DOC).
+ */
+export declare const EXTRACTION_VERSION = 2;
+/** `project_metadata` key holding the extraction version of the stored index. */
+export declare const EXTRACTION_VERSION_KEY = "extraction_version";
 /**
  * Progress callback for indexing operations
  */
@@ -28,6 +41,12 @@ export interface IndexResult {
     edgesCreated: number;
     errors: ExtractionError[];
     durationMs: number;
+    /**
+     * Files whose parse tree held an error region that may have swallowed
+     * declarations (`parse_error_region` warnings, REQ-HTMLLEX-003). Reported in
+     * the completion summary only; never persisted as a stat.
+     */
+    filesWithParseWarnings?: number;
 }
 /**
  * Result of a sync operation
@@ -40,6 +59,8 @@ export interface SyncResult {
     nodesUpdated: number;
     durationMs: number;
     changedFilePaths?: string[];
+    /** Changed files carrying `parse_error_region` warnings (REQ-HTMLLEX-003). */
+    filesWithParseWarnings?: number;
     /**
      * Spec links that transitioned into `drifted` during this sync's spec
      * pass (DRIFT-PUSH-DOC). Populated by SpecShip.sync(); absent when no
@@ -112,6 +133,22 @@ export declare class ExtractionOrchestrator {
      * inside a single run don't re-scan.
      */
     private ensureDetectedFrameworks;
+    /**
+     * True when the stored index was produced by an older extractor than
+     * {@link EXTRACTION_VERSION} (a missing stamp counts as stale), so files
+     * whose content hash still matches may hold dropped declarations
+     * (REQ-HTMLLEX-002).
+     */
+    private isExtractionStale;
+    /**
+     * Record that every stale file has been re-extracted by the current
+     * extractor. Called ONLY at the end of a complete full pass (sync /
+     * indexAll) — never from a file-scoped index, or a single-file auto-sync
+     * would mark recovery done while other files still miss declarations.
+     */
+    private stampExtractionVersion;
+    /** Whether a stored file must be re-extracted while the index is stale. */
+    private isStaleLanguage;
     /**
      * Index all files in the project
      */
@@ -121,16 +158,25 @@ export declare class ExtractionOrchestrator {
      */
     indexFiles(filePaths: string[]): Promise<IndexResult>;
     /**
-     * Index a single file
+     * Index a single file.
+     *
+     * `force` re-stores the extraction even when the content hash matches the
+     * stored file (stale-extraction recovery, REQ-HTMLLEX-002).
      */
-    indexFile(relativePath: string): Promise<ExtractionResult>;
+    indexFile(relativePath: string, options?: {
+        force?: boolean;
+    }): Promise<ExtractionResult>;
     /**
      * Index a single file with pre-read content and stats.
      * Used by the parallel batch reader to avoid redundant file I/O.
      */
-    indexFileWithContent(relativePath: string, content: string, stats: fs.Stats): Promise<ExtractionResult>;
+    indexFileWithContent(relativePath: string, content: string, stats: fs.Stats, force?: boolean): Promise<ExtractionResult>;
     /**
-     * Store extraction result in database
+     * Store extraction result in database.
+     *
+     * An unchanged content hash short-circuits the write unless `force` is set —
+     * the stale-extraction recovery (REQ-HTMLLEX-002) must replace a stored
+     * extraction whose hash is current but whose declarations were dropped.
      */
     private storeExtractionResult;
     /**

package/lib/dist/extraction/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/extraction/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AAKzB,OAAO,EAGL,gBAAgB,EAChB,eAAe,EAChB,MAAM,UAAU,CAAC;AAClB,OAAO,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAM7C,OAAe,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AA4BxC;;;;;;;;;GASG;AACH,eAAO,MAAM,kBAAkB,IAAI,CAAC;AAEpC,iFAAiF;AACjF,eAAO,MAAM,sBAAsB,uBAAuB,CAAC;AAa3D;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,UAAU,GAAG,SAAS,GAAG,SAAS,GAAG,WAAW,CAAC;IACxD,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED;;GAEG;AACH,MAAM,WAAW,WAAW;IAC1B,OAAO,EAAE,OAAO,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,UAAU,EAAE,MAAM,CAAC;IACnB;;;;OAIG;IACH,sBAAsB,CAAC,EAAE,MAAM,CAAC;CACjC;AAED;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,MAAM,CAAC;IACtB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;IACnB,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC5B,8EAA8E;IAC9E,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC;;;;OAIG;IACH,kBAAkB,CAAC,EAAE,OAAO,kCAAkC,EAAE,eAAe,EAAE,CAAC;IAClF;;;;OAIG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB;;;;OAIG;IACH,eAAe,CAAC,EAAE,OAAO,sBAAsB,EAAE,iBAAiB,CAAC;CACpE;AAED;;GAEG;AACH,wBAAgB,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAEnD;AAqED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAS1D;AAoJD;;;;;;GAMG;AACH,wBAAgB,aAAa,CAC3B,OAAO,EAAE,MAAM,EACf,UAAU,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,KAAK,IAAI,GACnD,MAAM,EAAE,CAkBV;AAED;;;GAGG;AACH,wBAAsB,kBAAkB,CACtC,OAAO,EAAE,MAAM,EACf,UAAU,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,KAAK,IAAI,GACnD,OAAO,CAAC,MAAM,EAAE,CAAC,CAoBnB;AAyHD;;GAEG;AACH,qBAAa,sBAAsB;IACjC,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,OAAO,CAAe;IAC9B;;;;;OAKG;IACH,OAAO,CAAC,sBAAsB,CAAyB;gBAE3C,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,YAAY;IAKlD;;;;;OAKG;IACH,OAAO,CAAC,qBAAqB;IAkD7B;;;;OAIG;IACH,OAAO,CAAC,wBAAwB;IAQhC;;;;;OAKG;IACH,OAAO,CAAC,iBAAiB;IAKzB;;;;;OAKG;IACH,OAAO,CAAC,sBAAsB;IAI9B,2EAA2E;IAC3E,OAAO,CAAC,eAAe;IAIvB;;OAEG;IACG,QAAQ,CACZ,UAAU,CAAC,EAAE,CAAC,QAAQ,EAAE,aAAa,KAAK,IAAI,EAC9C,MAAM,CAAC,EAAE,WAAW,EACpB,OAAO,CAAC,EAAE,OAAO,GAChB,OAAO,CAAC,WAAW,CAAC;IA6fvB;;OAEG;IACG,UAAU,CAAC,SAAS,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,WAAW,CAAC;IA6C3D;;;;;OAKG;IACG,SAAS,CAAC,YAAY,EAAE,MAAM,EAAE,OAAO,GAAE;QAAE,KAAK,CAAC,EAAE,OAAO,CAAA;KAAO,GAAG,OAAO,CAAC,gBAAgB,CAAC;IAuCnG;;;OAGG;IACG,oBAAoB,CACxB,YAAY,EAAE,MAAM,EACpB,OAAO,EAAE,MAAM,EACf,KAAK,EAAE,EAAE,CAAC,KAAK,EACf,KAAK,UAAQ,GACZ,OAAO,CAAC,gBAAgB,CAAC;IA0D5B;;;;;;OAMG;IACH,OAAO,CAAC,qBAAqB;IAuE7B;;;;;;;OAOG;IACG,IAAI,CAAC,UAAU,CAAC,EAAE,CAAC,QAAQ,EAAE,aAAa,KAAK,IAAI,GAAG,OAAO,CAAC,UAAU,CAAC;IAsJ/E;;;OAGG;IACH,eAAe,IAAI;QAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QAAC,QAAQ,EAAE,MAAM,EAAE,CAAC;QAAC,OAAO,EAAE,MAAM,EAAE,CAAA;KAAE;CAwF9E;AAGD,OAAO,EAAE,iBAAiB,EAAE,MAAM,eAAe,CAAC;AAClD,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,mBAAmB,EAAE,eAAe,EAAE,qBAAqB,EAAE,YAAY,EAAE,wBAAwB,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC"}

package/lib/dist/extraction/index.js

@@ -41,7 +41,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.loadAllGrammars = exports.loadGrammarsForLanguages = exports.initGrammars = exports.getSupportedLanguages = exports.isGrammarLoaded = exports.isLanguageSupported = exports.isSourceFile = exports.detectLanguage = exports.extractFromSource = exports.ExtractionOrchestrator = void 0;
+exports.loadAllGrammars = exports.loadGrammarsForLanguages = exports.initGrammars = exports.getSupportedLanguages = exports.isGrammarLoaded = exports.isLanguageSupported = exports.isSourceFile = exports.detectLanguage = exports.extractFromSource = exports.ExtractionOrchestrator = exports.EXTRACTION_VERSION_KEY = exports.EXTRACTION_VERSION = void 0;
 exports.hashContent = hashContent;
 exports.buildDefaultIgnore = buildDefaultIgnore;
 exports.scanDirectory = scanDirectory;
@@ -52,6 +52,7 @@ const path = __importStar(require("path"));
 const crypto = __importStar(require("crypto"));
 const child_process_1 = require("child_process");
 const tree_sitter_1 = require("./tree-sitter");
+const parse_warnings_1 = require("./parse-warnings");
 const grammars_1 = require("./grammars");
 const errors_1 = require("../errors");
 const utils_1 = require("../utils");
@@ -77,6 +78,29 @@ const PARSE_TIMEOUT_MS = 10_000;
  * This interval balances memory usage against the cost of reloading grammars.
  */
 const WORKER_RECYCLE_INTERVAL = 250;
+/**
+ * Version of the extractor's output. Bump it whenever an extraction fix
+ * changes what an UNCHANGED file produces (REQ-HTMLLEX-002): a stored index
+ * stamped with an older version is stale, and the next full sync / indexAll
+ * re-extracts every tracked file in {@link EXTRACTION_STALE_LANGUAGES} even
+ * though its content hash still matches.
+ *
+ * - 1 (implicit / missing): pre-HTMLLEX extraction.
+ * - 2: declarations survive `<!--` / `-->` inside JS/TS literals (HTMLLEX-DOC).
+ */
+exports.EXTRACTION_VERSION = 2;
+/** `project_metadata` key holding the extraction version of the stored index. */
+exports.EXTRACTION_VERSION_KEY = 'extraction_version';
+/**
+ * Languages whose stored extraction is invalidated by a version bump. Limited
+ * to the family the HTMLLEX fix touched to keep the one-off recovery cheap.
+ */
+const EXTRACTION_STALE_LANGUAGES = new Set([
+    'typescript',
+    'tsx',
+    'javascript',
+    'jsx',
+]);
 /**
  * Calculate SHA256 hash of file contents
  */
@@ -528,6 +552,29 @@ class ExtractionOrchestrator {
         this.detectedFrameworkNames = (0, frameworks_1.detectFrameworks)(context).map((r) => r.name);
         return this.detectedFrameworkNames;
     }
+    /**
+     * True when the stored index was produced by an older extractor than
+     * {@link EXTRACTION_VERSION} (a missing stamp counts as stale), so files
+     * whose content hash still matches may hold dropped declarations
+     * (REQ-HTMLLEX-002).
+     */
+    isExtractionStale() {
+        const stored = Number.parseInt(this.queries.getMetadata(exports.EXTRACTION_VERSION_KEY) ?? '', 10);
+        return !Number.isFinite(stored) || stored < exports.EXTRACTION_VERSION;
+    }
+    /**
+     * Record that every stale file has been re-extracted by the current
+     * extractor. Called ONLY at the end of a complete full pass (sync /
+     * indexAll) — never from a file-scoped index, or a single-file auto-sync
+     * would mark recovery done while other files still miss declarations.
+     */
+    stampExtractionVersion() {
+        this.queries.setMetadata(exports.EXTRACTION_VERSION_KEY, String(exports.EXTRACTION_VERSION));
+    }
+    /** Whether a stored file must be re-extracted while the index is stale. */
+    isStaleLanguage(language) {
+        return language !== undefined && EXTRACTION_STALE_LANGUAGES.has(language);
+    }
     /**
      * Index all files in the project
      */
@@ -564,6 +611,10 @@ class ExtractionOrchestrator {
         // between runs is picked up without restarting the process.
         this.detectedFrameworkNames = null;
         const frameworkNames = this.ensureDetectedFrameworks(files);
+        // REQ-HTMLLEX-002: a stored index from an older extractor holds files whose
+        // hash is current but whose declarations were dropped. Force re-extraction
+        // of the affected languages, then stamp once the pass completes.
+        const stale = this.isExtractionStale();
         if (signal?.aborted) {
             return {
                 success: false,
@@ -822,7 +873,7 @@ class ExtractionOrchestrator {
                 // Store in database on main thread (SQLite is not thread-safe)
                 if (result.nodes.length > 0 || result.errors.length === 0) {
                     const language = (0, grammars_1.detectLanguage)(filePath, content);
-                    this.storeExtractionResult(filePath, content, language, stats, result);
+                    this.storeExtractionResult(filePath, content, language, stats, result, stale && this.isStaleLanguage(language));
                 }
                 if (result.errors.length > 0) {
                     for (const err of result.errors) {
@@ -898,7 +949,7 @@ class ExtractionOrchestrator {
                 if (result.nodes.length > 0 || result.errors.length === 0) {
                     const language = (0, grammars_1.detectLanguage)(filePath, content);
                     const stats = await fsp.stat(path.join(this.rootDir, filePath));
-                    this.storeExtractionResult(filePath, content, language, stats, result);
+                    this.storeExtractionResult(filePath, content, language, stats, result, stale && this.isStaleLanguage(language));
                     const idx = errors.indexOf(errEntry);
                     if (idx >= 0)
                         errors.splice(idx, 1);
@@ -946,7 +997,7 @@ class ExtractionOrchestrator {
                     if (result.nodes.length > 0 || result.errors.length === 0) {
                         const language = (0, grammars_1.detectLanguage)(filePath, fullContent);
                         const stats = await fsp.stat(path.join(this.rootDir, filePath));
-                        this.storeExtractionResult(filePath, fullContent, language, stats, result);
+                        this.storeExtractionResult(filePath, fullContent, language, stats, result, stale && this.isStaleLanguage(language));
                         const idx = errors.indexOf(errEntry);
                         if (idx >= 0)
                             errors.splice(idx, 1);
@@ -964,6 +1015,14 @@ class ExtractionOrchestrator {
         if (parseWorker) {
             parseWorker.terminate().catch(() => { });
         }
+        // This complete pass (aborts return early above) re-extracted every stale
+        // file. A file that failed to read or parse is already reported in
+        // `errors`; parsing is deterministic, so retrying it on every sync would
+        // only re-extract the whole JS/TS tree forever (REQ-HTMLLEX-002.A2). It is
+        // re-extracted as soon as its content changes.
+        if (stale) {
+            this.stampExtractionVersion();
+        }
         return {
             success: filesIndexed > 0 || errors.filter((e) => e.severity === 'error').length === 0,
             filesIndexed,
@@ -973,6 +1032,7 @@ class ExtractionOrchestrator {
             edgesCreated: totalEdges,
             errors,
             durationMs: Date.now() - startTime,
+            filesWithParseWarnings: (0, parse_warnings_1.countParseWarningFiles)(errors),
         };
     }
     /**
@@ -1018,12 +1078,16 @@ class ExtractionOrchestrator {
             edgesCreated: totalEdges,
             errors,
             durationMs: Date.now() - startTime,
+            filesWithParseWarnings: (0, parse_warnings_1.countParseWarningFiles)(errors),
         };
     }
     /**
-     * Index a single file
+     * Index a single file.
+     *
+     * `force` re-stores the extraction even when the content hash matches the
+     * stored file (stale-extraction recovery, REQ-HTMLLEX-002).
      */
-    async indexFile(relativePath) {
+    async indexFile(relativePath, options = {}) {
         const fullPath = (0, utils_1.validatePathWithinRoot)(this.rootDir, relativePath);
         if (!fullPath) {
             return {
@@ -1057,13 +1121,13 @@ class ExtractionOrchestrator {
                 durationMs: 0,
             };
         }
-        return this.indexFileWithContent(relativePath, content, stats);
+        return this.indexFileWithContent(relativePath, content, stats, options.force ?? false);
     }
     /**
      * Index a single file with pre-read content and stats.
      * Used by the parallel batch reader to avoid redundant file I/O.
      */
-    async indexFileWithContent(relativePath, content, stats) {
+    async indexFileWithContent(relativePath, content, stats, force = false) {
         // Prevent path traversal
         const fullPath = (0, utils_1.validatePathWithinRoot)(this.rootDir, relativePath);
         if (!fullPath) {
@@ -1111,18 +1175,22 @@ class ExtractionOrchestrator {
         const result = (0, tree_sitter_1.extractFromSource)(relativePath, content, language, frameworkNames);
         // Store in database
         if (result.nodes.length > 0 || result.errors.length === 0) {
-            this.storeExtractionResult(relativePath, content, language, stats, result);
+            this.storeExtractionResult(relativePath, content, language, stats, result, force);
         }
         return result;
     }
     /**
-     * Store extraction result in database
+     * Store extraction result in database.
+     *
+     * An unchanged content hash short-circuits the write unless `force` is set —
+     * the stale-extraction recovery (REQ-HTMLLEX-002) must replace a stored
+     * extraction whose hash is current but whose declarations were dropped.
      */
-    storeExtractionResult(filePath, content, language, stats, result) {
+    storeExtractionResult(filePath, content, language, stats, result, force = false) {
         const contentHash = hashContent(content);
         // Check if file already exists and hasn't changed
         const existingFile = this.queries.getFileByPath(filePath);
-        if (existingFile && existingFile.contentHash === contentHash) {
+        if (!force && existingFile && existingFile.contentHash === contentHash) {
             return; // No changes
         }
         // Delete existing data for this file
@@ -1186,6 +1254,7 @@ class ExtractionOrchestrator {
         let filesChecked = 0;
         let filesAdded = 0;
         let filesModified = 0;
+        let filesWithParseWarnings = 0;
         let filesRemoved = 0;
         let nodesUpdated = 0;
         const changedFilePaths = [];
@@ -1195,6 +1264,10 @@ class ExtractionOrchestrator {
             total: 0,
         });
         const filesToIndex = [];
+        // REQ-HTMLLEX-002: files stored by an older extractor are re-extracted even
+        // though their size/mtime/hash still match. Computed once per pass.
+        const stale = this.isExtractionStale();
+        const forced = new Set();
         // === Filesystem reconcile (git-independent) ===
         // The source of truth for "what changed" is the filesystem vs the indexed
         // state — never git. We enumerate the current source files and reconcile
@@ -1225,6 +1298,15 @@ class ExtractionOrchestrator {
         for (const filePath of currentFiles) {
             const fullPath = path.join(this.rootDir, filePath);
             const tracked = trackedMap.get(filePath);
+            // (The existsSync guard skips files deleted on disk but still listed by
+            // `git ls-files` — the removal loop above already dropped them.)
+            if (stale && tracked && this.isStaleLanguage(tracked.language) && fs.existsSync(fullPath)) {
+                filesToIndex.push(filePath);
+                changedFilePaths.push(filePath);
+                forced.add(filePath);
+                filesModified++;
+                continue;
+            }
             // Cheap pre-filter: an already-indexed file whose size AND mtime both match
             // the DB is unchanged — skip it without reading or hashing. (A content
             // change that preserves both exactly is the blind spot every mtime-based
@@ -1282,11 +1364,21 @@ class ExtractionOrchestrator {
                 total,
                 currentFile: filePath,
             });
-            const result = await this.indexFile(filePath);
+            const force = forced.has(filePath);
+            const result = await this.indexFile(filePath, { force });
             nodesUpdated += result.nodes.length;
+            if ((0, parse_warnings_1.countParseWarningFiles)(result.errors) > 0)
+                filesWithParseWarnings++;
+        }
+        // Stamp once this full pass has re-extracted every stale file; a file that
+        // failed is reported in its result and is not retried on every sync
+        // (REQ-HTMLLEX-002.A2). File-scoped paths (indexFiles / indexFile) never stamp.
+        if (stale) {
+            this.stampExtractionVersion();
         }
         return {
             filesChecked,
+            filesWithParseWarnings,
             filesAdded,
             filesModified,
             filesRemoved,