kirograph 0.28.1 → 1.0.0

package/dist/core/pipeline.js

@@ -59,6 +59,8 @@ class IndexPipeline {
     let nodesCreated = 0;
     let edgesCreated = 0;
     const poisonedLanguages = /* @__PURE__ */ new Set();
+    const crashCounts = /* @__PURE__ */ new Map();
+    const POISON_THRESHOLD = 3;
     try {
       const files = await (0, import_sync.scanDirectory)(this.projectRoot, this.config, opts?.signal);
       opts?.onProgress?.({ phase: "scanning", current: files.length, total: files.length });
@@ -85,7 +87,7 @@ class IndexPipeline {
           const { detectLanguage } = await Promise.resolve().then(() => require("../extraction/languages.js"));
           const lang = detectLanguage(file);
           if (poisonedLanguages.has(lang)) continue;
-          const extracted = await (0, import_extractor.extractFile)(file, this.projectRoot, content, { enableComplexity: !!this.config.enableComplexity });
+          const extracted = await (0, import_extractor.extractFile)(file, this.projectRoot, content, { enableComplexity: !!this.config.enableComplexity, maxFileSize: this.config.maxFileSize });
           if (!extracted) continue;
           const oldNodes = this.db.getNodesByFile(extracted.filePath);
           if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map((n) => n.id));
@@ -113,6 +115,7 @@ class IndexPipeline {
             }
           });
           filesIndexed++;
+          crashCounts.set(lang, 0);
         } catch (err) {
           const msg = err instanceof Error ? err.message : String(err);
           errors.push(`${file}: ${msg}`);
@@ -120,11 +123,14 @@ class IndexPipeline {
           if (isWasmCrash) {
             const { detectLanguage } = await Promise.resolve().then(() => require("../extraction/languages.js"));
             const lang = detectLanguage(file);
-            poisonedLanguages.add(lang);
+            const count = (crashCounts.get(lang) ?? 0) + 1;
+            crashCounts.set(lang, count);
+            if (count >= POISON_THRESHOLD) {
+              poisonedLanguages.add(lang);
+            }
             (0, import_grammars.clearParserCache)();
             try {
               await (0, import_grammars.initGrammars)();
-              poisonedLanguages.clear();
             } catch {
               errors.push("WASM runtime unrecoverable after crash \u2014 aborting batch");
               break;
@@ -344,6 +350,8 @@ class IndexPipeline {
       result.filesScanned = result.filesScanned || filesToProcess.length;
       onProgress?.({ phase: "scanning", current: result.filesScanned, total: result.filesScanned });
       const poisonedLanguages = /* @__PURE__ */ new Set();
+      const crashCounts = /* @__PURE__ */ new Map();
+      const POISON_THRESHOLD = 3;
       for (let i = 0; i < filesToProcess.length; i++) {
         const file = filesToProcess[i];
         onProgress?.({ phase: "parsing", current: i + 1, total: filesToProcess.length, currentFile: file });
@@ -356,7 +364,7 @@ class IndexPipeline {
           const { detectLanguage } = await Promise.resolve().then(() => require("../extraction/languages.js"));
           const lang = detectLanguage(file);
           if (poisonedLanguages.has(lang)) continue;
-          const extracted = await (0, import_extractor.extractFile)(file, this.projectRoot, void 0, { enableComplexity: !!this.config.enableComplexity });
+          const extracted = await (0, import_extractor.extractFile)(file, this.projectRoot, void 0, { enableComplexity: !!this.config.enableComplexity, maxFileSize: this.config.maxFileSize });
           if (!extracted) continue;
           const existing = this.db.getFile(extracted.filePath);
           const isNew = !existing;
@@ -390,6 +398,7 @@ class IndexPipeline {
             }
           });
           this.resolver.invalidateFile(extracted.filePath);
+          crashCounts.set(lang, 0);
           if (isNew) result.added.push(extracted.filePath);
           else {
             result.modified.push(extracted.filePath);
@@ -402,11 +411,14 @@ class IndexPipeline {
           if (isWasmCrash) {
             const { detectLanguage } = await Promise.resolve().then(() => require("../extraction/languages.js"));
             const lang = detectLanguage(file);
-            poisonedLanguages.add(lang);
+            const count = (crashCounts.get(lang) ?? 0) + 1;
+            crashCounts.set(lang, count);
+            if (count >= POISON_THRESHOLD) {
+              poisonedLanguages.add(lang);
+            }
             (0, import_grammars.clearParserCache)();
             try {
               await (0, import_grammars.initGrammars)();
-              poisonedLanguages.clear();
             } catch {
               result.errors.push("WASM runtime unrecoverable after crash \u2014 aborting sync");
               break;

package/dist/core/pipeline.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/pipeline.ts"],
-  "sourcesContent": ["/**\n * IndexPipeline \u2014 full-index and incremental-sync pipelines.\n *\n * Owns the two heavy workflows:\n *   - indexAll(): scan all files, extract, store, resolve, detect frameworks,\n *                 generate embeddings, analyze architecture.\n *   - sync():     detect changed files via git (or full scan fallback),\n *                 re-extract only what changed, then run the same tail pipeline.\n *\n * Everything that touches the filesystem or sub-systems is injected via the\n * constructor, keeping this class testable and free of global state.\n */\n\nimport * as path from 'path';\nimport * as fs from 'fs';\nimport { GraphDatabase } from '../db/database';\nimport { scanDirectory, hashContent, getChangedFiles, shouldIncludeFile } from '../sync/index';\nimport { extractFile } from '../extraction/extractor';\nimport { clearParserCache, initGrammars, hasWasmGrammar } from '../extraction/grammars';\nimport { detectFrameworks } from '../frameworks/index';\nimport { ReferenceResolver } from '../resolution/index';\nimport { VectorManager } from '../vectors/index';\nimport { ArchitectureAnalyzer } from '../architecture/index';\nimport type { KiroGraphConfig } from '../config';\nimport type { IndexResult, IndexProgress, SyncResult } from '../types';\nimport { LockManager } from './lock-manager';\nimport { Mutex } from '../utils';\n\nconst FILE_IO_BATCH_SIZE = 10;\n\nexport class IndexPipeline {\n  private readonly mutex = new Mutex();\n\n  constructor(\n    private readonly db: GraphDatabase,\n    private readonly vectors: VectorManager,\n    private readonly resolver: ReferenceResolver,\n    private readonly arch: ArchitectureAnalyzer,\n    private readonly lock: LockManager,\n    private readonly config: KiroGraphConfig,\n    private readonly projectRoot: string,\n  ) {}\n\n  async indexAll(opts?: {\n    onProgress?: (p: IndexProgress) => void;\n    force?: boolean;\n    signal?: AbortSignal;\n  }): Promise<IndexResult> {\n    const release = await this.mutex.acquire();\n    this.lock.acquire();\n    const start = Date.now();\n    const errors: string[] = [];\n    let filesIndexed = 0;\n    let nodesCreated = 0;\n    let edgesCreated = 0;\n\n    // Track languages whose WASM parser is currently poisoned (ABORT=true on the module).\n    // Once a language's parser aborts, every subsequent parse call for that language\n    // fails instantly. We skip those files until clearParserCache + initGrammars succeeds.\n    const poisonedLanguages = new Set<string>();\n\n    try {\n      const files = await scanDirectory(this.projectRoot, this.config, opts?.signal);\n      opts?.onProgress?.({ phase: 'scanning', current: files.length, total: files.length });\n\n      // Batch-read files in parallel\n      const contentMap = new Map<string, Buffer>();\n      for (let b = 0; b < files.length; b += FILE_IO_BATCH_SIZE) {\n        const batch = files.slice(b, b + FILE_IO_BATCH_SIZE);\n        const results = await Promise.all(batch.map(f => fs.promises.readFile(f).catch(() => null)));\n        for (let i = 0; i < batch.length; i++) {\n          if (results[i]) contentMap.set(batch[i], results[i]!);\n        }\n      }\n\n      for (let i = 0; i < files.length; i++) {\n        const file = files[i];\n        opts?.onProgress?.({ phase: 'parsing', current: i + 1, total: files.length, currentFile: file });\n\n        try {\n          const content = contentMap.get(file);\n          if (!content) continue;\n          if (content.length > this.config.maxFileSize) continue;\n\n          const relPath = path.relative(this.projectRoot, file).replace(/\\\\/g, '/');\n\n          if (!opts?.force) {\n            const existing = this.db.getFile(relPath);\n            if (existing && hashContent(content) === existing.contentHash) continue;\n          }\n\n          // Skip files whose language parser is currently poisoned\n          const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n          const lang = detectLanguage(file);\n          if (poisonedLanguages.has(lang)) continue;\n\n          const extracted = await extractFile(file, this.projectRoot, content, { enableComplexity: !!(this.config as any).enableComplexity });\n          if (!extracted) continue;\n\n          const oldNodes = this.db.getNodesByFile(extracted.filePath);\n          if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n          this.db.transaction(() => {\n            this.db.deleteNodesByFile(extracted.filePath);\n            this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n            this.db.upsertFile({\n              path: extracted.filePath,\n              contentHash: extracted.contentHash,\n              language: extracted.language,\n              fileSize: extracted.fileSize,\n              symbolCount: extracted.nodes.length,\n              indexedAt: Date.now(),\n            });\n            for (const node of extracted.nodes) { this.db.upsertNode(node); nodesCreated++; }\n            for (const edge of extracted.edges) { this.db.insertEdge(edge); edgesCreated++; }\n            for (const ref of extracted.unresolvedRefs) {\n              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n            }\n          });\n\n          filesIndexed++;\n        } catch (err) {\n          const msg = err instanceof Error ? err.message : String(err);\n          errors.push(`${file}: ${msg}`);\n\n          // Detect WASM runtime abort and attempt recovery\n          const isWasmCrash = (err as any)?.constructor?.name === 'RuntimeError'\n            || msg.includes('Aborted(') \n            || msg.includes('RuntimeError')\n            || msg.includes('WASM grammar exists but failed to load');\n          if (isWasmCrash) {\n            // Mark the language as poisoned so we skip remaining files of this language\n            const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n            const lang = detectLanguage(file);\n            poisonedLanguages.add(lang);\n\n            clearParserCache();\n            try {\n              await initGrammars();\n              // Recovery succeeded \u2014 un-poison all languages\n              poisonedLanguages.clear();\n            } catch {\n              errors.push('WASM runtime unrecoverable after crash \u2014 aborting batch');\n              break;\n            }\n          }\n        }\n      }\n\n      // Re-process files that have symbolCount=0 but should have symbols (WASM recovery)\n      const emptyFiles = this.db.getAllFiles().filter(\n        (f: any) => f.symbolCount === 0 && hasWasmGrammar(f.language)\n      );\n      if (emptyFiles.length > 0) {\n        opts?.onProgress?.({ phase: 'retrying', current: 0, total: emptyFiles.length });\n        for (let i = 0; i < emptyFiles.length; i++) {\n          const ef = emptyFiles[i];\n          const absPath = path.join(this.projectRoot, ef.path);\n          opts?.onProgress?.({ phase: 'retrying', current: i + 1, total: emptyFiles.length, currentFile: absPath });\n          try {\n            const extracted = await extractFile(absPath, this.projectRoot, undefined, { enableComplexity: !!(this.config as any).enableComplexity });\n            if (!extracted || extracted.nodes.length === 0) continue;\n\n            const oldNodes = this.db.getNodesByFile(extracted.filePath);\n            if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n            this.db.transaction(() => {\n              this.db.deleteNodesByFile(extracted.filePath);\n              this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n              this.db.upsertFile({\n                path: extracted.filePath,\n                contentHash: extracted.contentHash,\n                language: extracted.language,\n                fileSize: extracted.fileSize,\n                symbolCount: extracted.nodes.length,\n                indexedAt: Date.now(),\n              });\n              for (const node of extracted.nodes) { this.db.upsertNode(node); nodesCreated++; }\n              for (const edge of extracted.edges) { this.db.insertEdge(edge); edgesCreated++; }\n              for (const ref of extracted.unresolvedRefs) {\n                this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n              }\n            });\n            filesIndexed++;\n          } catch {\n            // Already logged in first pass or genuinely broken \u2014 skip\n          }\n        }\n      }\n\n      // Resolve cross-file references\n      opts?.onProgress?.({ phase: 'resolving', current: 0, total: 1 });\n      await this.resolver.resolveAll((current, total) => {\n        opts?.onProgress?.({ phase: 'resolving', current, total });\n      });\n\n      // Detect frameworks\n      opts?.onProgress?.({ phase: 'detecting frameworks', current: 0, total: 1 });\n      const detectedFrameworks = await detectFrameworks(this.projectRoot, this.db);\n      const languages = [...new Set(this.db.getAllFiles().map(f => (f as any).language).filter(Boolean))];\n      opts?.onProgress?.({\n        phase: 'detecting frameworks', current: 1, total: 1,\n        meta: { frameworks: detectedFrameworks.map(f => f.name), languages },\n      });\n\n      // Generate embeddings (if enabled)\n      if (this.vectors.isInitialized()) {\n        opts?.onProgress?.({ phase: 'embeddings', current: 0, total: 1 });\n        await this.vectors.embedAll((current, total) =>\n          opts?.onProgress?.({ phase: 'embeddings', current, total })\n        );\n      }\n\n      // Analyze architecture (if enabled, or auto-enabled for security)\n      if (this.config.enableArchitecture || this.config.enableSecurity) {\n        if (this.config.enableSecurity && !this.config.enableArchitecture) {\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          logWarn('enableSecurity requires enableArchitecture \u2014 auto-enabling architecture analysis for this run');\n        }\n        opts?.onProgress?.({ phase: 'architecture', current: 0, total: 1 });\n        await this.arch.analyze(msg =>\n          opts?.onProgress?.({ phase: 'architecture', current: 0, total: 1, meta: { msg } })\n        );\n        opts?.onProgress?.({ phase: 'architecture', current: 1, total: 1 });\n      }\n\n      // Run security analysis (if enabled)\n      if (this.config.enableSecurity) {\n        try {\n          const { SecurityPipeline } = await Promise.resolve().then(() => require('../security/pipeline.js'));\n          this.db.applySecuritySchema();\n          const secPipeline = new SecurityPipeline(this.db, this.config, this.projectRoot);\n          opts?.onProgress?.({ phase: 'security', current: 0, total: 1 });\n          await secPipeline.run((phase, current, total) =>\n            opts?.onProgress?.({ phase: 'security', current, total, meta: { secPhase: phase } })\n          );\n          opts?.onProgress?.({ phase: 'security', current: 1, total: 1 });\n        } catch { /* security analysis is non-critical */ }\n      }\n\n      // Index documentation (if enabled)\n      if (this.config.enableDocs) {\n        try {\n          const { DocsIndexer } = await Promise.resolve().then(() => require('../docs/indexer.js'));\n          this.db.applyDocsSchema();\n          const docsIndexer = new DocsIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await docsIndexer.indexAll({\n            force: opts?.force,\n            onProgress: msg => opts?.onProgress?.({ phase: 'docs', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\n      }\n\n      // Index data files (if enabled)\n      if ((this.config as any).enableData) {\n        try {\n          const { DataIndexer } = await Promise.resolve().then(() => require('../data/indexer.js'));\n          this.db.applyDataSchema();\n          const dataIndexer = new DataIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await dataIndexer.indexAll({\n            onProgress: msg => opts?.onProgress?.({ phase: 'data', current: 0, total: 1, meta: { msg } }),\n          });\n\n          // Assign data files to 'data' architecture layer if architecture is enabled\n          if (this.config.enableArchitecture) {\n            try {\n              const rawDb = this.db.getRawDb();\n              // Check if arch_file_layers table exists\n              const tableExists = rawDb.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='arch_file_layers'\");\n              if (tableExists) {\n                const datasets = rawDb.all('SELECT file_path FROM data_datasets') as Array<{ file_path: string }>;\n                for (const ds of datasets) {\n                  rawDb.run(\n                    `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence) VALUES (?, ?, ?)`,\n                    [ds.file_path, 'layer:data', 1.0],\n                  );\n                }\n              }\n            } catch { /* non-critical */ }\n          }\n        } catch { /* data indexing is non-critical */ }\n      }\n\n      // Index pattern matches (if enabled)\n      if ((this.config as any).enablePatterns) {\n        try {\n          this.db.applyPatternsSchema();\n          const { PatternIndexer } = await Promise.resolve().then(() => require('../patterns/indexer.js'));\n          const indexer = new PatternIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await indexer.indexAll((phase, current, total) => {\n            opts?.onProgress?.({ phase: 'patterns' as any, current, total });\n          });\n        } catch (err) {\n          // Patterns are non-critical \u2014 log and continue\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          const msg = err instanceof Error ? err.message : String(err);\n          logWarn(`[patterns] Pattern indexing failed (non-critical): ${msg}`);\n        }\n      }\n\n      this.lock.clearDirty();\n      return { success: errors.length === 0, filesIndexed, nodesCreated, edgesCreated, errors, duration: Date.now() - start };\n    } finally {\n      this.lock.release();\n      release();\n    }\n  }\n\n  async sync(opts?: {\n    changedFiles?: string[];\n    onProgress?: (p: IndexProgress) => void;\n  }): Promise<SyncResult> {\n    const release = await this.mutex.acquire();\n    this.lock.acquire();\n    const start = Date.now();\n    const changedFiles = opts?.changedFiles;\n    const onProgress = opts?.onProgress;\n    const result: SyncResult = {\n      added: [], modified: [], removed: [],\n      nodesCreated: 0, nodesUpdated: 0, nodesRemoved: 0,\n      edgesCreated: 0, edgesRemoved: 0,\n      filesScanned: 0, errors: [], duration: 0,\n    };\n\n    try {\n      const removeFile = async (rel: string) => {\n        const oldNodes = this.db.getNodesByFile(rel);\n        const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map(n => n.id)).length;\n        result.nodesRemoved += oldNodes.length;\n        result.edgesRemoved += oldEdgeCount;\n        await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n        this.db.deleteFile(rel);\n        this.db.deleteUnresolvedRefsByFile(rel);\n        // Clean up pattern matches for removed files (only if patterns are enabled)\n        if ((this.config as any).enablePatterns) {\n          this.db.getRawDb().run('DELETE FROM pattern_matches WHERE file_path = ?', [rel]);\n        }\n        result.removed.push(rel);\n      };\n\n      // \u2500\u2500 Exclude-rule cleanup \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n      // Remove any indexed files that now match the current exclude patterns.\n      // This handles the case where a user adds a new exclude pattern (e.g.\n      // \"**/.vite/**\") and expects those files to disappear from the index on\n      // the next sync without needing a full --force re-index.\n      const allIndexed = this.db.getAllFiles();\n      for (const f of allIndexed) {\n        if (!shouldIncludeFile(f.path, this.config)) {\n          onProgress?.({ phase: 'scanning', current: 0, total: 0, meta: { excludeCleanup: true, file: f.path } });\n          await removeFile(f.path);\n        }\n      }\n\n      let filesToProcess: string[];\n\n      onProgress?.({ phase: 'scanning', current: 0, total: 0 });\n\n      if (changedFiles) {\n        filesToProcess = changedFiles.map(f => path.resolve(this.projectRoot, f));\n      } else {\n        const gitChanged = await getChangedFiles(this.projectRoot, this.config);\n        const hasChanges = gitChanged.added.length > 0 || gitChanged.modified.length > 0 || gitChanged.removed.length > 0;\n\n        if (hasChanges) {\n          for (const p of gitChanged.removed) {\n            await removeFile(path.relative(this.projectRoot, p).replace(/\\\\/g, '/'));\n          }\n          filesToProcess = [...gitChanged.added, ...gitChanged.modified];\n        } else {\n          // Fallback: full scan + detect removed files\n          const indexed = new Set(this.db.getAllFiles().map(f => f.path));\n          const current = new Set(\n            (await scanDirectory(this.projectRoot, this.config))\n              .map(f => path.relative(this.projectRoot, f).replace(/\\\\/g, '/'))\n          );\n          result.filesScanned = current.size;\n          for (const p of indexed) {\n            if (!current.has(p)) await removeFile(p);\n          }\n          filesToProcess = await scanDirectory(this.projectRoot, this.config);\n        }\n      }\n\n      result.filesScanned = result.filesScanned || filesToProcess.length;\n      onProgress?.({ phase: 'scanning', current: result.filesScanned, total: result.filesScanned });\n\n      const poisonedLanguages = new Set<string>();\n\n      for (let i = 0; i < filesToProcess.length; i++) {\n        const file = filesToProcess[i];\n        onProgress?.({ phase: 'parsing', current: i + 1, total: filesToProcess.length, currentFile: file });\n\n        if (!fs.existsSync(file)) {\n          const rel = path.relative(this.projectRoot, file).replace(/\\\\/g, '/');\n          await removeFile(rel);\n          continue;\n        }\n\n        try {\n          // Skip files whose language parser is currently poisoned\n          const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n          const lang = detectLanguage(file);\n          if (poisonedLanguages.has(lang)) continue;\n\n          const extracted = await extractFile(file, this.projectRoot, undefined, { enableComplexity: !!(this.config as any).enableComplexity });\n          if (!extracted) continue;\n\n          const existing = this.db.getFile(extracted.filePath);\n          const isNew = !existing;\n          if (!isNew && existing!.contentHash === extracted.contentHash) continue;\n\n          const oldNodes = this.db.getNodesByFile(extracted.filePath);\n          const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map(n => n.id)).length;\n          await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n          this.db.transaction(() => {\n            result.nodesRemoved += oldNodes.length;\n            result.edgesRemoved += oldEdgeCount;\n            this.db.deleteNodesByFile(extracted.filePath);\n            this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n            this.db.upsertFile({\n              path: extracted.filePath,\n              contentHash: extracted.contentHash,\n              language: extracted.language,\n              fileSize: extracted.fileSize,\n              symbolCount: extracted.nodes.length,\n              indexedAt: Date.now(),\n            });\n            for (const node of extracted.nodes) { this.db.upsertNode(node); result.nodesCreated++; }\n            for (const edge of extracted.edges) { this.db.insertEdge(edge); result.edgesCreated++; }\n            for (const ref of extracted.unresolvedRefs) {\n              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n            }\n          });\n\n          this.resolver.invalidateFile(extracted.filePath);\n          if (isNew) result.added.push(extracted.filePath);\n          else { result.modified.push(extracted.filePath); result.nodesUpdated += extracted.nodes.length; }\n        } catch (err) {\n          const msg = err instanceof Error ? err.message : String(err);\n          result.errors.push(`${file}: ${msg}`);\n\n          // Detect WASM runtime abort and attempt recovery\n          const isWasmCrash = (err as any)?.constructor?.name === 'RuntimeError'\n            || msg.includes('Aborted(') \n            || msg.includes('RuntimeError')\n            || msg.includes('WASM grammar exists but failed to load');\n          if (isWasmCrash) {\n            const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n            const lang = detectLanguage(file);\n            poisonedLanguages.add(lang);\n\n            clearParserCache();\n            try {\n              await initGrammars();\n              poisonedLanguages.clear();\n            } catch {\n              result.errors.push('WASM runtime unrecoverable after crash \u2014 aborting sync');\n              break;\n            }\n          }\n        }\n      }\n\n      // Resolve cross-file references\n      onProgress?.({ phase: 'resolving', current: 0, total: 1 });\n      await this.resolver.resolveAll((current, total) => {\n        onProgress?.({ phase: 'resolving', current, total });\n      });\n\n      await detectFrameworks(this.projectRoot);\n\n      // Generate embeddings (if enabled)\n      if (this.vectors.isInitialized()) {\n        onProgress?.({ phase: 'embeddings', current: 0, total: 1 });\n        await this.vectors.embedAll((current, total) =>\n          onProgress?.({ phase: 'embeddings', current, total })\n        );\n      }\n\n      // Analyze architecture (if enabled, or auto-enabled for security)\n      if (this.config.enableArchitecture || this.config.enableSecurity) {\n        if (this.config.enableSecurity && !this.config.enableArchitecture) {\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          logWarn('enableSecurity requires enableArchitecture \u2014 auto-enabling architecture analysis for this run');\n        }\n        onProgress?.({ phase: 'architecture', current: 0, total: 1 });\n        await this.arch.analyze(msg =>\n          onProgress?.({ phase: 'architecture', current: 0, total: 1, meta: { msg } })\n        );\n        onProgress?.({ phase: 'architecture', current: 1, total: 1 });\n      }\n\n      // Run security analysis (if enabled)\n      if (this.config.enableSecurity) {\n        try {\n          const { SecurityPipeline } = await Promise.resolve().then(() => require('../security/pipeline.js'));\n          this.db.applySecuritySchema();\n          const secPipeline = new SecurityPipeline(this.db, this.config, this.projectRoot);\n          onProgress?.({ phase: 'security', current: 0, total: 1 });\n          await secPipeline.run((phase, current, total) =>\n            onProgress?.({ phase: 'security', current, total, meta: { secPhase: phase } })\n          );\n          onProgress?.({ phase: 'security', current: 1, total: 1 });\n        } catch { /* security analysis is non-critical */ }\n      }\n\n      // Re-index documentation (if enabled)\n      if (this.config.enableDocs) {\n        try {\n          const { DocsIndexer } = await Promise.resolve().then(() => require('../docs/indexer.js'));\n          this.db.applyDocsSchema();\n          const docsIndexer = new DocsIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await docsIndexer.indexAll({\n            onProgress: msg => onProgress?.({ phase: 'docs', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\n      }\n\n      // Re-index data files (if enabled)\n      if ((this.config as any).enableData) {\n        try {\n          const { DataIndexer } = await Promise.resolve().then(() => require('../data/indexer.js'));\n          this.db.applyDataSchema();\n          const dataIndexer = new DataIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await dataIndexer.indexAll({\n            onProgress: msg => onProgress?.({ phase: 'data', current: 0, total: 1, meta: { msg } }),\n          });\n\n          // Assign data files to 'data' architecture layer if architecture is enabled\n          if (this.config.enableArchitecture) {\n            try {\n              const rawDb = this.db.getRawDb();\n              const tableExists = rawDb.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='arch_file_layers'\");\n              if (tableExists) {\n                const datasets = rawDb.all('SELECT file_path FROM data_datasets') as Array<{ file_path: string }>;\n                for (const ds of datasets) {\n                  rawDb.run(\n                    `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence) VALUES (?, ?, ?)`,\n                    [ds.file_path, 'layer:data', 1.0],\n                  );\n                }\n              }\n            } catch { /* non-critical */ }\n          }\n        } catch { /* data indexing is non-critical */ }\n      }\n\n      // Re-index pattern matches for changed files (if enabled)\n      if ((this.config as any).enablePatterns) {\n        try {\n          const tableExists = this.db.getRawDb().get(\n            \"SELECT name FROM sqlite_master WHERE type='table' AND name='pattern_matches'\"\n          );\n          if (tableExists) {\n            const { PatternIndexer } = await Promise.resolve().then(() => require('../patterns/indexer.js'));\n            const { PatternLibraryLoader } = await Promise.resolve().then(() => require('../patterns/loader.js'));\n            const { PatternRunner } = await Promise.resolve().then(() => require('../patterns/runner.js'));\n            const runner = new PatternRunner();\n            if (runner.isAvailable()) {\n              const loader = new PatternLibraryLoader();\n              const builtinPath = require('path').join(__dirname, '../patterns/library');\n              const rules = loader.load(builtinPath, (this.config as any).patternLibraryPath);\n              const threshold = (this.config as any).patternSeverityThreshold ?? 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+  "sourcesContent": ["/**\n * IndexPipeline \u2014 full-index and incremental-sync pipelines.\n *\n * Owns the two heavy workflows:\n *   - indexAll(): scan all files, extract, store, resolve, detect frameworks,\n *                 generate embeddings, analyze architecture.\n *   - sync():     detect changed files via git (or full scan fallback),\n *                 re-extract only what changed, then run the same tail pipeline.\n *\n * Everything that touches the filesystem or sub-systems is injected via the\n * constructor, keeping this class testable and free of global state.\n */\n\nimport * as path from 'path';\nimport * as fs from 'fs';\nimport { GraphDatabase } from '../db/database';\nimport { scanDirectory, hashContent, getChangedFiles, shouldIncludeFile } from '../sync/index';\nimport { extractFile } from '../extraction/extractor';\nimport { clearParserCache, initGrammars, hasWasmGrammar } from '../extraction/grammars';\nimport { detectFrameworks } from '../frameworks/index';\nimport { ReferenceResolver } from '../resolution/index';\nimport { VectorManager } from '../vectors/index';\nimport { ArchitectureAnalyzer } from '../architecture/index';\nimport type { KiroGraphConfig } from '../config';\nimport type { IndexResult, IndexProgress, SyncResult } from '../types';\nimport { LockManager } from './lock-manager';\nimport { Mutex } from '../utils';\n\nconst FILE_IO_BATCH_SIZE = 10;\n\nexport class IndexPipeline {\n  private readonly mutex = new Mutex();\n\n  constructor(\n    private readonly db: GraphDatabase,\n    private readonly vectors: VectorManager,\n    private readonly resolver: ReferenceResolver,\n    private readonly arch: ArchitectureAnalyzer,\n    private readonly lock: LockManager,\n    private readonly config: KiroGraphConfig,\n    private readonly projectRoot: string,\n  ) {}\n\n  async indexAll(opts?: {\n    onProgress?: (p: IndexProgress) => void;\n    force?: boolean;\n    signal?: AbortSignal;\n  }): Promise<IndexResult> {\n    const release = await this.mutex.acquire();\n    this.lock.acquire();\n    const start = Date.now();\n    const errors: string[] = [];\n    let filesIndexed = 0;\n    let nodesCreated = 0;\n    let edgesCreated = 0;\n\n    // Track languages whose WASM parser is currently poisoned (ABORT=true on the module).\n    // Once a language's parser aborts, every subsequent parse call for that language\n    // fails instantly. We skip those files until clearParserCache + initGrammars succeeds.\n    const poisonedLanguages = new Set<string>();\n    // Track consecutive WASM crashes per language. Only poison after threshold is exceeded.\n    const crashCounts = new Map<string, number>();\n    const POISON_THRESHOLD = 3;\n\n    try {\n      const files = await scanDirectory(this.projectRoot, this.config, opts?.signal);\n      opts?.onProgress?.({ phase: 'scanning', current: files.length, total: files.length });\n\n      // Batch-read files in parallel\n      const contentMap = new Map<string, Buffer>();\n      for (let b = 0; b < files.length; b += FILE_IO_BATCH_SIZE) {\n        const batch = files.slice(b, b + FILE_IO_BATCH_SIZE);\n        const results = await Promise.all(batch.map(f => fs.promises.readFile(f).catch(() => null)));\n        for (let i = 0; i < batch.length; i++) {\n          if (results[i]) contentMap.set(batch[i], results[i]!);\n        }\n      }\n\n      for (let i = 0; i < files.length; i++) {\n        const file = files[i];\n        opts?.onProgress?.({ phase: 'parsing', current: i + 1, total: files.length, currentFile: file });\n\n        try {\n          const content = contentMap.get(file);\n          if (!content) continue;\n          if (content.length > this.config.maxFileSize) continue;\n\n          const relPath = path.relative(this.projectRoot, file).replace(/\\\\/g, '/');\n\n          if (!opts?.force) {\n            const existing = this.db.getFile(relPath);\n            if (existing && hashContent(content) === existing.contentHash) continue;\n          }\n\n          // Skip files whose language parser is currently poisoned\n          const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n          const lang = detectLanguage(file);\n          if (poisonedLanguages.has(lang)) continue;\n\n          const extracted = await extractFile(file, this.projectRoot, content, { enableComplexity: !!(this.config as any).enableComplexity, maxFileSize: this.config.maxFileSize });\n          if (!extracted) continue;\n\n          const oldNodes = this.db.getNodesByFile(extracted.filePath);\n          if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n          this.db.transaction(() => {\n            this.db.deleteNodesByFile(extracted.filePath);\n            this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n            this.db.upsertFile({\n              path: extracted.filePath,\n              contentHash: extracted.contentHash,\n              language: extracted.language,\n              fileSize: extracted.fileSize,\n              symbolCount: extracted.nodes.length,\n              indexedAt: Date.now(),\n            });\n            for (const node of extracted.nodes) { this.db.upsertNode(node); nodesCreated++; }\n            for (const edge of extracted.edges) { this.db.insertEdge(edge); edgesCreated++; }\n            for (const ref of extracted.unresolvedRefs) {\n              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n            }\n          });\n\n          filesIndexed++;\n          // Reset crash count on successful parse for this language\n          crashCounts.set(lang, 0);\n        } catch (err) {\n          const msg = err instanceof Error ? err.message : String(err);\n          errors.push(`${file}: ${msg}`);\n\n          // Detect WASM runtime abort and attempt recovery\n          const isWasmCrash = (err as any)?.constructor?.name === 'RuntimeError'\n            || msg.includes('Aborted(') \n            || msg.includes('RuntimeError')\n            || msg.includes('WASM grammar exists but failed to load');\n          if (isWasmCrash) {\n            const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n            const lang = detectLanguage(file);\n            const count = (crashCounts.get(lang) ?? 0) + 1;\n            crashCounts.set(lang, count);\n\n            // Only poison the language after multiple consecutive crashes\n            if (count >= POISON_THRESHOLD) {\n              poisonedLanguages.add(lang);\n            }\n\n            clearParserCache();\n            try {\n              await initGrammars();\n              // Recovery succeeded \u2014 WASM runtime is usable again.\n              // Languages with count >= POISON_THRESHOLD remain permanently disabled\n              // for this run. Other languages (below threshold) were never poisoned\n              // and continue parsing normally.\n            } catch {\n              errors.push('WASM runtime unrecoverable after crash \u2014 aborting batch');\n              break;\n            }\n          }\n        }\n      }\n\n      // Re-process files that have symbolCount=0 but should have symbols (WASM recovery)\n      const emptyFiles = this.db.getAllFiles().filter(\n        (f: any) => f.symbolCount === 0 && hasWasmGrammar(f.language)\n      );\n      if (emptyFiles.length > 0) {\n        opts?.onProgress?.({ phase: 'retrying', current: 0, total: emptyFiles.length });\n        for (let i = 0; i < emptyFiles.length; i++) {\n          const ef = emptyFiles[i];\n          const absPath = path.join(this.projectRoot, ef.path);\n          opts?.onProgress?.({ phase: 'retrying', current: i + 1, total: emptyFiles.length, currentFile: absPath });\n          try {\n            const extracted = await extractFile(absPath, this.projectRoot, undefined, { enableComplexity: !!(this.config as any).enableComplexity });\n            if (!extracted || extracted.nodes.length === 0) continue;\n\n            const oldNodes = this.db.getNodesByFile(extracted.filePath);\n            if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n            this.db.transaction(() => {\n              this.db.deleteNodesByFile(extracted.filePath);\n              this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n              this.db.upsertFile({\n                path: extracted.filePath,\n                contentHash: extracted.contentHash,\n                language: extracted.language,\n                fileSize: extracted.fileSize,\n                symbolCount: extracted.nodes.length,\n                indexedAt: Date.now(),\n              });\n              for (const node of extracted.nodes) { this.db.upsertNode(node); nodesCreated++; }\n              for (const edge of extracted.edges) { this.db.insertEdge(edge); edgesCreated++; }\n              for (const ref of extracted.unresolvedRefs) {\n                this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n              }\n            });\n            filesIndexed++;\n          } catch {\n            // Already logged in first pass or genuinely broken \u2014 skip\n          }\n        }\n      }\n\n      // Resolve cross-file references\n      opts?.onProgress?.({ phase: 'resolving', current: 0, total: 1 });\n      await this.resolver.resolveAll((current, total) => {\n        opts?.onProgress?.({ phase: 'resolving', current, total });\n      });\n\n      // Detect frameworks\n      opts?.onProgress?.({ phase: 'detecting frameworks', current: 0, total: 1 });\n      const detectedFrameworks = await detectFrameworks(this.projectRoot, this.db);\n      const languages = [...new Set(this.db.getAllFiles().map(f => (f as any).language).filter(Boolean))];\n      opts?.onProgress?.({\n        phase: 'detecting frameworks', current: 1, total: 1,\n        meta: { frameworks: detectedFrameworks.map(f => f.name), languages },\n      });\n\n      // Generate embeddings (if enabled)\n      if (this.vectors.isInitialized()) {\n        opts?.onProgress?.({ phase: 'embeddings', current: 0, total: 1 });\n        await this.vectors.embedAll((current, total) =>\n          opts?.onProgress?.({ phase: 'embeddings', current, total })\n        );\n      }\n\n      // Analyze architecture (if enabled, or auto-enabled for security)\n      if (this.config.enableArchitecture || this.config.enableSecurity) {\n        if (this.config.enableSecurity && !this.config.enableArchitecture) {\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          logWarn('enableSecurity requires enableArchitecture \u2014 auto-enabling architecture analysis for this run');\n        }\n        opts?.onProgress?.({ phase: 'architecture', current: 0, total: 1 });\n        await this.arch.analyze(msg =>\n          opts?.onProgress?.({ phase: 'architecture', current: 0, total: 1, meta: { msg } })\n        );\n        opts?.onProgress?.({ phase: 'architecture', current: 1, total: 1 });\n      }\n\n      // Run security analysis (if enabled)\n      if (this.config.enableSecurity) {\n        try {\n          const { SecurityPipeline } = await Promise.resolve().then(() => require('../security/pipeline.js'));\n          this.db.applySecuritySchema();\n          const secPipeline = new SecurityPipeline(this.db, this.config, this.projectRoot);\n          opts?.onProgress?.({ phase: 'security', current: 0, total: 1 });\n          await secPipeline.run((phase, current, total) =>\n            opts?.onProgress?.({ phase: 'security', current, total, meta: { secPhase: phase } })\n          );\n          opts?.onProgress?.({ phase: 'security', current: 1, total: 1 });\n        } catch { /* security analysis is non-critical */ }\n      }\n\n      // Index documentation (if enabled)\n      if (this.config.enableDocs) {\n        try {\n          const { DocsIndexer } = await Promise.resolve().then(() => require('../docs/indexer.js'));\n          this.db.applyDocsSchema();\n          const docsIndexer = new DocsIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await docsIndexer.indexAll({\n            force: opts?.force,\n            onProgress: msg => opts?.onProgress?.({ phase: 'docs', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\n      }\n\n      // Index data files (if enabled)\n      if ((this.config as any).enableData) {\n        try {\n          const { DataIndexer } = await Promise.resolve().then(() => require('../data/indexer.js'));\n          this.db.applyDataSchema();\n          const dataIndexer = new DataIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await dataIndexer.indexAll({\n            onProgress: msg => opts?.onProgress?.({ phase: 'data', current: 0, total: 1, meta: { msg } }),\n          });\n\n          // Assign data files to 'data' architecture layer if architecture is enabled\n          if (this.config.enableArchitecture) {\n            try {\n              const rawDb = this.db.getRawDb();\n              // Check if arch_file_layers table exists\n              const tableExists = rawDb.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='arch_file_layers'\");\n              if (tableExists) {\n                const datasets = rawDb.all('SELECT file_path FROM data_datasets') as Array<{ file_path: string }>;\n                for (const ds of datasets) {\n                  rawDb.run(\n                    `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence) VALUES (?, ?, ?)`,\n                    [ds.file_path, 'layer:data', 1.0],\n                  );\n                }\n              }\n            } catch { /* non-critical */ }\n          }\n        } catch { /* data indexing is non-critical */ }\n      }\n\n      // Index pattern matches (if enabled)\n      if ((this.config as any).enablePatterns) {\n        try {\n          this.db.applyPatternsSchema();\n          const { PatternIndexer } = await Promise.resolve().then(() => require('../patterns/indexer.js'));\n          const indexer = new PatternIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await indexer.indexAll((phase, current, total) => {\n            opts?.onProgress?.({ phase: 'patterns' as any, current, total });\n          });\n        } catch (err) {\n          // Patterns are non-critical \u2014 log and continue\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          const msg = err instanceof Error ? err.message : String(err);\n          logWarn(`[patterns] Pattern indexing failed (non-critical): ${msg}`);\n        }\n      }\n\n      this.lock.clearDirty();\n      return { success: errors.length === 0, filesIndexed, nodesCreated, edgesCreated, errors, duration: Date.now() - start };\n    } finally {\n      this.lock.release();\n      release();\n    }\n  }\n\n  async sync(opts?: {\n    changedFiles?: string[];\n    onProgress?: (p: IndexProgress) => void;\n  }): Promise<SyncResult> {\n    const release = await this.mutex.acquire();\n    this.lock.acquire();\n    const start = Date.now();\n    const changedFiles = opts?.changedFiles;\n    const onProgress = opts?.onProgress;\n    const result: SyncResult = {\n      added: [], modified: [], removed: [],\n      nodesCreated: 0, nodesUpdated: 0, nodesRemoved: 0,\n      edgesCreated: 0, edgesRemoved: 0,\n      filesScanned: 0, errors: [], duration: 0,\n    };\n\n    try {\n      const removeFile = async (rel: string) => {\n        const oldNodes = this.db.getNodesByFile(rel);\n        const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map(n => n.id)).length;\n        result.nodesRemoved += oldNodes.length;\n        result.edgesRemoved += oldEdgeCount;\n        await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n        this.db.deleteFile(rel);\n        this.db.deleteUnresolvedRefsByFile(rel);\n        // Clean up pattern matches for removed files (only if patterns are enabled)\n        if ((this.config as any).enablePatterns) {\n          this.db.getRawDb().run('DELETE FROM pattern_matches WHERE file_path = ?', [rel]);\n        }\n        result.removed.push(rel);\n      };\n\n      // \u2500\u2500 Exclude-rule cleanup \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n      // Remove any indexed files that now match the current exclude patterns.\n      // This handles the case where a user adds a new exclude pattern (e.g.\n      // \"**/.vite/**\") and expects those files to disappear from the index on\n      // the next sync without needing a full --force re-index.\n      const allIndexed = this.db.getAllFiles();\n      for (const f of allIndexed) {\n        if (!shouldIncludeFile(f.path, this.config)) {\n          onProgress?.({ phase: 'scanning', current: 0, total: 0, meta: { excludeCleanup: true, file: f.path } });\n          await removeFile(f.path);\n        }\n      }\n\n      let filesToProcess: string[];\n\n      onProgress?.({ phase: 'scanning', current: 0, total: 0 });\n\n      if (changedFiles) {\n        filesToProcess = changedFiles.map(f => path.resolve(this.projectRoot, f));\n      } else {\n        const gitChanged = await getChangedFiles(this.projectRoot, this.config);\n        const hasChanges = gitChanged.added.length > 0 || gitChanged.modified.length > 0 || gitChanged.removed.length > 0;\n\n        if (hasChanges) {\n          for (const p of gitChanged.removed) {\n            await removeFile(path.relative(this.projectRoot, p).replace(/\\\\/g, '/'));\n          }\n          filesToProcess = [...gitChanged.added, ...gitChanged.modified];\n        } else {\n          // Fallback: full scan + detect removed files\n          const indexed = new Set(this.db.getAllFiles().map(f => f.path));\n          const current = new Set(\n            (await scanDirectory(this.projectRoot, this.config))\n              .map(f => path.relative(this.projectRoot, f).replace(/\\\\/g, '/'))\n          );\n          result.filesScanned = current.size;\n          for (const p of indexed) {\n            if (!current.has(p)) await removeFile(p);\n          }\n          filesToProcess = await scanDirectory(this.projectRoot, this.config);\n        }\n      }\n\n      result.filesScanned = result.filesScanned || filesToProcess.length;\n      onProgress?.({ phase: 'scanning', current: result.filesScanned, total: result.filesScanned });\n\n      const poisonedLanguages = new Set<string>();\n      const crashCounts = new Map<string, number>();\n      const POISON_THRESHOLD = 3;\n\n      for (let i = 0; i < filesToProcess.length; i++) {\n        const file = filesToProcess[i];\n        onProgress?.({ phase: 'parsing', current: i + 1, total: filesToProcess.length, currentFile: file });\n\n        if (!fs.existsSync(file)) {\n          const rel = path.relative(this.projectRoot, file).replace(/\\\\/g, '/');\n          await removeFile(rel);\n          continue;\n        }\n\n        try {\n          // Skip files whose language parser is currently poisoned\n          const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n          const lang = detectLanguage(file);\n          if (poisonedLanguages.has(lang)) continue;\n\n          const extracted = await extractFile(file, this.projectRoot, undefined, { enableComplexity: !!(this.config as any).enableComplexity, maxFileSize: this.config.maxFileSize });\n          if (!extracted) continue;\n\n          const existing = this.db.getFile(extracted.filePath);\n          const isNew = !existing;\n          if (!isNew && existing!.contentHash === extracted.contentHash) continue;\n\n          const oldNodes = this.db.getNodesByFile(extracted.filePath);\n          const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map(n => n.id)).length;\n          await this.vectors.deleteEmbeddings(oldNodes.map(n => n.id));\n\n          this.db.transaction(() => {\n            result.nodesRemoved += oldNodes.length;\n            result.edgesRemoved += oldEdgeCount;\n            this.db.deleteNodesByFile(extracted.filePath);\n            this.db.deleteUnresolvedRefsByFile(extracted.filePath);\n            this.db.upsertFile({\n              path: extracted.filePath,\n              contentHash: extracted.contentHash,\n              language: extracted.language,\n              fileSize: extracted.fileSize,\n              symbolCount: extracted.nodes.length,\n              indexedAt: Date.now(),\n            });\n            for (const node of extracted.nodes) { this.db.upsertNode(node); result.nodesCreated++; }\n            for (const edge of extracted.edges) { this.db.insertEdge(edge); result.edgesCreated++; }\n            for (const ref of extracted.unresolvedRefs) {\n              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);\n            }\n          });\n\n          this.resolver.invalidateFile(extracted.filePath);\n          // Reset crash count on successful parse for this language\n          crashCounts.set(lang, 0);\n          if (isNew) result.added.push(extracted.filePath);\n          else { result.modified.push(extracted.filePath); result.nodesUpdated += extracted.nodes.length; }\n        } catch (err) {\n          const msg = err instanceof Error ? err.message : String(err);\n          result.errors.push(`${file}: ${msg}`);\n\n          // Detect WASM runtime abort and attempt recovery\n          const isWasmCrash = (err as any)?.constructor?.name === 'RuntimeError'\n            || msg.includes('Aborted(') \n            || msg.includes('RuntimeError')\n            || msg.includes('WASM grammar exists but failed to load');\n          if (isWasmCrash) {\n            const { detectLanguage } = await Promise.resolve().then(() => require('../extraction/languages.js'));\n            const lang = detectLanguage(file);\n            const count = (crashCounts.get(lang) ?? 0) + 1;\n            crashCounts.set(lang, count);\n\n            if (count >= POISON_THRESHOLD) {\n              poisonedLanguages.add(lang);\n            }\n\n            clearParserCache();\n            try {\n              await initGrammars();\n              // Recovery succeeded \u2014 WASM runtime is usable again.\n              // Languages at POISON_THRESHOLD stay disabled for this run.\n            } catch {\n              result.errors.push('WASM runtime unrecoverable after crash \u2014 aborting sync');\n              break;\n            }\n          }\n        }\n      }\n\n      // Resolve cross-file references\n      onProgress?.({ phase: 'resolving', current: 0, total: 1 });\n      await this.resolver.resolveAll((current, total) => {\n        onProgress?.({ phase: 'resolving', current, total });\n      });\n\n      await detectFrameworks(this.projectRoot);\n\n      // Generate embeddings (if enabled)\n      if (this.vectors.isInitialized()) {\n        onProgress?.({ phase: 'embeddings', current: 0, total: 1 });\n        await this.vectors.embedAll((current, total) =>\n          onProgress?.({ phase: 'embeddings', current, total })\n        );\n      }\n\n      // Analyze architecture (if enabled, or auto-enabled for security)\n      if (this.config.enableArchitecture || this.config.enableSecurity) {\n        if (this.config.enableSecurity && !this.config.enableArchitecture) {\n          const { logWarn } = await Promise.resolve().then(() => require('../errors.js'));\n          logWarn('enableSecurity requires enableArchitecture \u2014 auto-enabling architecture analysis for this run');\n        }\n        onProgress?.({ phase: 'architecture', current: 0, total: 1 });\n        await this.arch.analyze(msg =>\n          onProgress?.({ phase: 'architecture', current: 0, total: 1, meta: { msg } })\n        );\n        onProgress?.({ phase: 'architecture', current: 1, total: 1 });\n      }\n\n      // Run security analysis (if enabled)\n      if (this.config.enableSecurity) {\n        try {\n          const { SecurityPipeline } = await Promise.resolve().then(() => require('../security/pipeline.js'));\n          this.db.applySecuritySchema();\n          const secPipeline = new SecurityPipeline(this.db, this.config, this.projectRoot);\n          onProgress?.({ phase: 'security', current: 0, total: 1 });\n          await secPipeline.run((phase, current, total) =>\n            onProgress?.({ phase: 'security', current, total, meta: { secPhase: phase } })\n          );\n          onProgress?.({ phase: 'security', current: 1, total: 1 });\n        } catch { /* security analysis is non-critical */ }\n      }\n\n      // Re-index documentation (if enabled)\n      if (this.config.enableDocs) {\n        try {\n          const { DocsIndexer } = await Promise.resolve().then(() => require('../docs/indexer.js'));\n          this.db.applyDocsSchema();\n          const docsIndexer = new DocsIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await docsIndexer.indexAll({\n            onProgress: msg => onProgress?.({ phase: 'docs', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\n      }\n\n      // Re-index data files (if enabled)\n      if ((this.config as any).enableData) {\n        try {\n          const { DataIndexer } = await Promise.resolve().then(() => require('../data/indexer.js'));\n          this.db.applyDataSchema();\n          const dataIndexer = new DataIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n          await dataIndexer.indexAll({\n            onProgress: msg => onProgress?.({ phase: 'data', current: 0, total: 1, meta: { msg } }),\n          });\n\n          // Assign data files to 'data' architecture layer if architecture is enabled\n          if (this.config.enableArchitecture) {\n            try {\n              const rawDb = this.db.getRawDb();\n              const tableExists = rawDb.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='arch_file_layers'\");\n              if (tableExists) {\n                const datasets = rawDb.all('SELECT file_path FROM data_datasets') as Array<{ file_path: string }>;\n                for (const ds of datasets) {\n                  rawDb.run(\n                    `INSERT OR REPLACE INTO arch_file_layers (file_path, layer_id, confidence) VALUES (?, ?, ?)`,\n                    [ds.file_path, 'layer:data', 1.0],\n                  );\n                }\n              }\n            } catch { /* non-critical */ }\n          }\n        } catch { /* data indexing is non-critical */ }\n      }\n\n      // Re-index pattern matches for changed files (if enabled)\n      if ((this.config as any).enablePatterns) {\n        try {\n          const tableExists = this.db.getRawDb().get(\n            \"SELECT name FROM sqlite_master WHERE type='table' AND name='pattern_matches'\"\n          );\n          if (tableExists) {\n            const { PatternIndexer } = await Promise.resolve().then(() => require('../patterns/indexer.js'));\n            const { PatternLibraryLoader } = await Promise.resolve().then(() => require('../patterns/loader.js'));\n            const { PatternRunner } = await Promise.resolve().then(() => require('../patterns/runner.js'));\n            const runner = new PatternRunner();\n            if (runner.isAvailable()) {\n              const loader = new PatternLibraryLoader();\n              const builtinPath = require('path').join(__dirname, '../patterns/library');\n              const rules = loader.load(builtinPath, (this.config as any).patternLibraryPath);\n              const threshold = (this.config as any).patternSeverityThreshold ?? 'low';\n              const indexer = new PatternIndexer(this.db.getRawDb(), this.config, this.projectRoot);\n              const changedPaths = [...result.added, ...result.modified];\n              for (const filePath of changedPaths) {\n                const fileRecord = this.db.getFile(filePath);\n                const language = fileRecord?.language ?? 'unknown';\n                await indexer.indexFile(filePath, language, rules, runner, threshold, Date.now());\n              }\n            }\n          }\n        } catch { /* non-critical */ }\n      }\n\n      this.lock.clearDirty();\n      result.duration = Date.now() - start;\n      return result;\n    } finally {\n      this.lock.release();\n      release();\n    }\n  }\n}\n"],
+  "mappings": 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   "names": []
 }

package/dist/extraction/extractor.js

@@ -66,6 +66,18 @@ async function extractFile(filePath, projectRoot, content, opts) {
   } catch {
     return null;
   }
+  if (opts?.maxFileSize !== void 0 && Buffer.byteLength(source, "utf8") > opts.maxFileSize) {
+    const relPathSkip = path.relative(projectRoot, filePath).replace(/\\/g, "/");
+    return {
+      filePath: relPathSkip,
+      language,
+      contentHash: crypto.createHash("sha256").update(source).digest("hex"),
+      fileSize: Buffer.byteLength(source, "utf8"),
+      nodes: [],
+      edges: [],
+      unresolvedRefs: []
+    };
+  }
   if (language === "jupyter") {
     return (0, import_notebook.extractNotebook)(filePath, projectRoot, source);
   }
@@ -88,7 +100,36 @@ async function extractFile(filePath, projectRoot, content, opts) {
     }
     throw new Error(`Parser unavailable for ${language} (WASM grammar exists but failed to load)`);
   }
-  const tree = parser.parse(source);
+  if (language === "yaml" && source.includes("{{")) {
+    return {
+      filePath: relPath,
+      language,
+      contentHash,
+      fileSize,
+      nodes: [],
+      edges: [],
+      unresolvedRefs: []
+    };
+  }
+  let tree;
+  try {
+    tree = parser.parse(source);
+  } catch (parseErr) {
+    const parseMsg = parseErr?.message ?? String(parseErr);
+    const isWasmCrash = parseErr?.constructor?.name === "RuntimeError" || parseMsg.includes("memory access out of bounds") || parseMsg.includes("Aborted(");
+    if (isWasmCrash) {
+      return {
+        filePath: relPath,
+        language,
+        contentHash,
+        fileSize,
+        nodes: [],
+        edges: [],
+        unresolvedRefs: []
+      };
+    }
+    throw parseErr;
+  }
   const nodes = [];
   const edges = [];
   const unresolvedRefs = [];
@@ -251,6 +292,8 @@ const KIND_MAP = {
   // Java, C#
   // Classes / structs
   class_declaration: "class",
+  abstract_class_declaration: "class",
+  // TypeScript `abstract class` (distinct AST node from class_declaration)
   class_expression: "class",
   class_definition: "class",
   // Python, Scala
@@ -403,6 +446,7 @@ function walkTree(node, source, filePath, language, nodes, edges, unresolvedRefs
         isExported: isExported(node),
         isAsync: isAsync(node),
         isStatic: isStatic(node),
+        isAbstract: isAbstract(node),
         updatedAt: now
       };
       nodes.push(graphNode);
@@ -821,6 +865,19 @@ function isStatic(node) {
   }
   return false;
 }
+function isAbstract(node) {
+  if (node.type === "abstract_class_declaration") return true;
+  for (let i = 0; i < node.childCount; i++) {
+    const child = node.child(i);
+    if (child.type === "abstract") return true;
+    if (child.type === "modifiers") {
+      for (let j = 0; j < child.childCount; j++) {
+        if (child.child(j).type === "abstract") return true;
+      }
+    }
+  }
+  return false;
+}
 const CALL_NODE_TYPES = /* @__PURE__ */ new Set([
   "call_expression",
   // JS/TS/Go/Rust/Swift/Kotlin/Dart/C/C++