kirograph 0.20.1 → 0.23.0

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);\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);\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\n        this.db.getRawDb().run('DELETE FROM pattern_matches WHERE file_path = ?', [rel]);\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);\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 ?? '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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+  "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);\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);\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);\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 ?? '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/data/indexer.js

@@ -99,7 +99,7 @@ class DataIndexer {
     const profiler = new import_profiler.ColumnProfiler();
     const allRows = [];
     const maxRows = this.config.dataMaxRows ?? 1e6;
-    const { columns, totalRows } = await parser.parse(absPath, {
+    const { columns, totalRows, metadataJson } = await parser.parse(absPath, {
       maxRows,
       onBatch: (rows, cols) => {
         profiler.addBatch(rows, cols);
@@ -115,9 +115,9 @@ class DataIndexer {
       this.db.run("DELETE FROM data_columns WHERE dataset_id = ?", [datasetId]);
       this.db.run("DELETE FROM data_datasets WHERE id = ?", [datasetId]);
       this.db.run(`
-        INSERT INTO data_datasets (id, file_path, format, row_count, column_count, file_size, content_hash, summary, indexed_at)
-        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
-      `, [datasetId, relPath, parser.name, totalRows, columns.length, stat.size, contentHash, null, Date.now()]);
+        INSERT INTO data_datasets (id, file_path, format, row_count, column_count, file_size, content_hash, summary, indexed_at, metadata_json)
+        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+      `, [datasetId, relPath, parser.name, totalRows, columns.length, stat.size, contentHash, null, Date.now(), metadataJson ?? null]);
       for (const col of columnProfiles) {
         this.db.run(`
           INSERT INTO data_columns (id, dataset_id, name, position, inferred_type, nullable, null_count, null_pct, cardinality, min_value, max_value, mean_value, sample_values, summary, updated_at)

package/dist/data/indexer.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/data/indexer.ts"],
-  "sourcesContent": ["/**\n * Data Indexer\n *\n * Orchestrates: scan data files \u2192 parse \u2192 profile columns \u2192 persist rows to SQLite.\n * Supports incremental re-indexing via content hashes.\n */\n\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport * as crypto from 'crypto';\nimport picomatch from 'picomatch';\nimport type { KiroGraphConfig } from '../config';\nimport type { DataSet, DataColumn, DataIndexResult, ParsedRow } from './types';\nimport { getDataParser } from './parsers/index';\nimport { ColumnProfiler } from './profiler';\n\n/**\n * Generate a dataset ID from a file path.\n * Slugifies the relative path: tests/fixtures/users.csv \u2192 tests-fixtures-users\n */\nfunction generateDatasetId(filePath: string): string {\n  return filePath\n    .replace(/\\.[^.]+$/, '')  // remove extension\n    .replace(/[/\\\\]/g, '-')   // replace path separators\n    .replace(/[^a-zA-Z0-9-_]/g, '-') // replace special chars\n    .replace(/-+/g, '-')      // collapse multiple dashes\n    .replace(/^-|-$/g, '')    // trim leading/trailing dashes\n    .toLowerCase();\n}\n\nexport class DataIndexer {\n  private readonly db: any;\n  private readonly config: KiroGraphConfig;\n  private readonly projectRoot: string;\n\n  constructor(db: any, config: KiroGraphConfig, projectRoot: string) {\n    this.db = db;\n    this.config = config;\n    this.projectRoot = projectRoot;\n  }\n\n  async indexAll(opts?: { force?: boolean; onProgress?: (msg: string) => void }): Promise<DataIndexResult> {\n    const start = Date.now();\n    const result: DataIndexResult = {\n      datasetsIndexed: 0, rowsIndexed: 0, columnsProfiled: 0, errors: [], duration: 0,\n    };\n\n    const files = this.scanDataFiles();\n    opts?.onProgress?.(`data: found ${files.length} data files`);\n\n    for (const relPath of files) {\n      try {\n        const indexed = await this.indexFile(relPath, opts?.force ?? false);\n        if (indexed) {\n          result.datasetsIndexed++;\n          result.rowsIndexed += indexed.rows;\n          result.columnsProfiled += indexed.columns;\n        }\n      } catch (err) {\n        result.errors.push(`${relPath}: ${err instanceof Error ? err.message : String(err)}`);\n      }\n    }\n\n    // Remove datasets for files that no longer exist\n    this.removeDeletedDatasets(files);\n\n    // Link data files to code (if enabled)\n    if ((this.config as any).dataLinkCode !== false && result.datasetsIndexed > 0) {\n      try {\n        const { DataCodeLinker } = await Promise.resolve().then(() => require('./linker.js'));\n        const linker = new DataCodeLinker(this.db, this.projectRoot);\n        const refsCreated = linker.linkAll();\n        opts?.onProgress?.(`data: linked ${refsCreated} code references`);\n      } catch {\n        // Non-critical \u2014 linking failure shouldn't block indexing\n      }\n    }\n\n    result.duration = Date.now() - start;\n    return result;\n  }\n\n  async indexFile(relPath: string, force = false): Promise<{ rows: number; columns: number } | null> {\n    const absPath = path.join(this.projectRoot, relPath);\n    if (!fs.existsSync(absPath)) return null;\n\n    const stat = fs.statSync(absPath);\n    if (stat.size > (this.config as any).dataMaxFileSize) return null;\n\n    // Check content hash for incremental\n    const fileBuffer = fs.readFileSync(absPath);\n    const contentHash = crypto.createHash('sha256').update(fileBuffer).digest('hex');\n\n    const datasetId = generateDatasetId(relPath);\n\n    if (!force) {\n      const existing = this.db.get('SELECT content_hash FROM data_datasets WHERE id = ?', [datasetId]);\n      if (existing?.content_hash === contentHash) return null; // unchanged\n    }\n\n    // Get parser\n    const parser = getDataParser(relPath);\n    if (!parser) return null;\n\n    // Parse and profile\n    const profiler = new ColumnProfiler();\n    const allRows: ParsedRow[] = [];\n    const maxRows = (this.config as any).dataMaxRows ?? 1_000_000;\n\n    const { columns, totalRows } = await parser.parse(absPath, {\n      maxRows,\n      onBatch: (rows, cols) => {\n        profiler.addBatch(rows, cols);\n        allRows.push(...rows);\n      },\n    });\n\n    if (columns.length === 0) return null;\n\n    // Finalize profiles\n    const columnProfiles = profiler.finalize(datasetId);\n\n    // Persist in transaction\n    this.db.run('BEGIN');\n    try {\n      // Delete old dataset data\n      const rowTableName = `data_rows_${datasetId.replace(/[^a-zA-Z0-9_]/g, '_')}`;\n      this.db.run(`DROP TABLE IF EXISTS \"${rowTableName}\"`);\n      this.db.run('DELETE FROM data_columns WHERE dataset_id = ?', [datasetId]);\n      this.db.run('DELETE FROM data_datasets WHERE id = ?', [datasetId]);\n\n      // Insert dataset\n      this.db.run(`\n        INSERT INTO data_datasets (id, file_path, format, row_count, column_count, file_size, content_hash, summary, indexed_at)\n        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)\n      `, [datasetId, relPath, parser.name, totalRows, columns.length, stat.size, contentHash, null, Date.now()]);\n\n      // Insert column profiles\n      for (const col of columnProfiles) {\n        this.db.run(`\n          INSERT INTO data_columns (id, dataset_id, name, position, inferred_type, nullable, null_count, null_pct, cardinality, min_value, max_value, mean_value, sample_values, summary, updated_at)\n          VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n        `, [\n          col.id, col.datasetId, col.name, col.position, col.inferredType,\n          col.nullable ? 1 : 0, col.nullCount, col.nullPct, col.cardinality,\n          col.minValue, col.maxValue, col.meanValue,\n          JSON.stringify(col.sampleValues), col.summary, col.updatedAt,\n        ]);\n      }\n\n      // Create row table with dynamic schema\n      const colDefs = columns.map(c => `\"${c.replace(/\"/g, '\"\"')}\" TEXT`).join(', ');\n      this.db.run(`CREATE TABLE \"${rowTableName}\" (rowid INTEGER PRIMARY KEY AUTOINCREMENT, ${colDefs})`);\n\n      // Insert rows in batches\n      const colNames = columns.map(c => `\"${c.replace(/\"/g, '\"\"')}\"`).join(', ');\n      const placeholders = columns.map(() => '?').join(', ');\n      const insertStmt = `INSERT INTO \"${rowTableName}\" (${colNames}) VALUES (${placeholders})`;\n\n      for (const row of allRows) {\n        const values = columns.map(c => {\n          const v = row[c];\n          if (v === null || v === undefined) return null;\n          if (typeof v === 'object') return JSON.stringify(v);\n          return v;\n        });\n        this.db.run(insertStmt, values);\n      }\n\n      // Save history snapshot for drift detection\n      const historyColumns = columnProfiles.map(col => ({\n        name: col.name,\n        type: col.inferredType,\n        cardinality: col.cardinality,\n        nullPct: col.nullPct,\n      }));\n      this.db.run(`\n        INSERT INTO data_dataset_history (dataset_id, snapshot_at, row_count, column_count, columns_json, content_hash)\n        VALUES (?, ?, ?, ?, ?, ?)\n      `, [datasetId, Date.now(), totalRows, columns.length, JSON.stringify(historyColumns), contentHash]);\n\n      this.db.run('COMMIT');\n    } catch (err) {\n      this.db.run('ROLLBACK');\n      throw err;\n    }\n\n    return { rows: totalRows, columns: columns.length };\n  }\n\n  // \u2500\u2500 Private \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\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n  private scanDataFiles(): string[] {\n    const includePatterns = (this.config as any).dataInclude ?? [];\n    const excludePatterns = (this.config as any).dataExclude ?? [];\n    const includeMatchers = includePatterns.map((p: string) => picomatch(p));\n    const excludeMatchers = excludePatterns.map((p: string) => picomatch(p));\n    const results: string[] = [];\n\n    const walk = (dir: string) => {\n      let entries: fs.Dirent[];\n      try { entries = fs.readdirSync(dir, { withFileTypes: true }); } catch { return; }\n\n      for (const entry of entries) {\n        const full = path.join(dir, entry.name);\n        const rel = path.relative(this.projectRoot, full).replace(/\\\\/g, '/');\n\n        if (entry.isDirectory()) {\n          if (excludeMatchers.some((m: any) => m(rel + '/'))) continue;\n          walk(full);\n        } else if (entry.isFile()) {\n          if (excludeMatchers.some((m: any) => m(rel))) continue;\n          if (includeMatchers.some((m: any) => m(rel))) {\n            // Verify a parser exists for this format\n            if (getDataParser(rel)) {\n              results.push(rel);\n            }\n          }\n        }\n      }\n    };\n\n    walk(this.projectRoot);\n    return results;\n  }\n\n  private removeDeletedDatasets(currentFiles: string[]): void {\n    const currentSet = new Set(currentFiles.map(f => generateDatasetId(f)));\n    const indexed = (this.db.all('SELECT id FROM data_datasets') as Array<{ id: string }>).map(r => r.id);\n\n    for (const id of indexed) {\n      if (!currentSet.has(id)) {\n        const rowTableName = `data_rows_${id.replace(/[^a-zA-Z0-9_]/g, '_')}`;\n        this.db.run(`DROP TABLE IF EXISTS \"${rowTableName}\"`);\n        this.db.run('DELETE FROM data_columns WHERE dataset_id = ?', [id]);\n        this.db.run('DELETE FROM data_code_refs WHERE dataset_id = ?', [id]);\n        this.db.run('DELETE FROM data_datasets WHERE id = ?', [id]);\n      }\n    }\n  }\n}\n"],
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+  "sourcesContent": ["/**\n * Data Indexer\n *\n * Orchestrates: scan data files \u2192 parse \u2192 profile columns \u2192 persist rows to SQLite.\n * Supports incremental re-indexing via content hashes.\n */\n\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport * as crypto from 'crypto';\nimport picomatch from 'picomatch';\nimport type { KiroGraphConfig } from '../config';\nimport type { DataSet, DataColumn, DataIndexResult, ParsedRow } from './types';\nimport { getDataParser } from './parsers/index';\nimport { ColumnProfiler } from './profiler';\n\n/**\n * Generate a dataset ID from a file path.\n * Slugifies the relative path: tests/fixtures/users.csv \u2192 tests-fixtures-users\n */\nfunction generateDatasetId(filePath: string): string {\n  return filePath\n    .replace(/\\.[^.]+$/, '')  // remove extension\n    .replace(/[/\\\\]/g, '-')   // replace path separators\n    .replace(/[^a-zA-Z0-9-_]/g, '-') // replace special chars\n    .replace(/-+/g, '-')      // collapse multiple dashes\n    .replace(/^-|-$/g, '')    // trim leading/trailing dashes\n    .toLowerCase();\n}\n\nexport class DataIndexer {\n  private readonly db: any;\n  private readonly config: KiroGraphConfig;\n  private readonly projectRoot: string;\n\n  constructor(db: any, config: KiroGraphConfig, projectRoot: string) {\n    this.db = db;\n    this.config = config;\n    this.projectRoot = projectRoot;\n  }\n\n  async indexAll(opts?: { force?: boolean; onProgress?: (msg: string) => void }): Promise<DataIndexResult> {\n    const start = Date.now();\n    const result: DataIndexResult = {\n      datasetsIndexed: 0, rowsIndexed: 0, columnsProfiled: 0, errors: [], duration: 0,\n    };\n\n    const files = this.scanDataFiles();\n    opts?.onProgress?.(`data: found ${files.length} data files`);\n\n    for (const relPath of files) {\n      try {\n        const indexed = await this.indexFile(relPath, opts?.force ?? false);\n        if (indexed) {\n          result.datasetsIndexed++;\n          result.rowsIndexed += indexed.rows;\n          result.columnsProfiled += indexed.columns;\n        }\n      } catch (err) {\n        result.errors.push(`${relPath}: ${err instanceof Error ? err.message : String(err)}`);\n      }\n    }\n\n    // Remove datasets for files that no longer exist\n    this.removeDeletedDatasets(files);\n\n    // Link data files to code (if enabled)\n    if ((this.config as any).dataLinkCode !== false && result.datasetsIndexed > 0) {\n      try {\n        const { DataCodeLinker } = await Promise.resolve().then(() => require('./linker.js'));\n        const linker = new DataCodeLinker(this.db, this.projectRoot);\n        const refsCreated = linker.linkAll();\n        opts?.onProgress?.(`data: linked ${refsCreated} code references`);\n      } catch {\n        // Non-critical \u2014 linking failure shouldn't block indexing\n      }\n    }\n\n    result.duration = Date.now() - start;\n    return result;\n  }\n\n  async indexFile(relPath: string, force = false): Promise<{ rows: number; columns: number } | null> {\n    const absPath = path.join(this.projectRoot, relPath);\n    if (!fs.existsSync(absPath)) return null;\n\n    const stat = fs.statSync(absPath);\n    if (stat.size > (this.config as any).dataMaxFileSize) return null;\n\n    // Check content hash for incremental\n    const fileBuffer = fs.readFileSync(absPath);\n    const contentHash = crypto.createHash('sha256').update(fileBuffer).digest('hex');\n\n    const datasetId = generateDatasetId(relPath);\n\n    if (!force) {\n      const existing = this.db.get('SELECT content_hash FROM data_datasets WHERE id = ?', [datasetId]);\n      if (existing?.content_hash === contentHash) return null; // unchanged\n    }\n\n    // Get parser\n    const parser = getDataParser(relPath);\n    if (!parser) return null;\n\n    // Parse and profile\n    const profiler = new ColumnProfiler();\n    const allRows: ParsedRow[] = [];\n    const maxRows = (this.config as any).dataMaxRows ?? 1_000_000;\n\n    const { columns, totalRows, metadataJson } = await parser.parse(absPath, {\n      maxRows,\n      onBatch: (rows, cols) => {\n        profiler.addBatch(rows, cols);\n        allRows.push(...rows);\n      },\n    });\n\n    if (columns.length === 0) return null;\n\n    // Finalize profiles\n    const columnProfiles = profiler.finalize(datasetId);\n\n    // Persist in transaction\n    this.db.run('BEGIN');\n    try {\n      // Delete old dataset data\n      const rowTableName = `data_rows_${datasetId.replace(/[^a-zA-Z0-9_]/g, '_')}`;\n      this.db.run(`DROP TABLE IF EXISTS \"${rowTableName}\"`);\n      this.db.run('DELETE FROM data_columns WHERE dataset_id = ?', [datasetId]);\n      this.db.run('DELETE FROM data_datasets WHERE id = ?', [datasetId]);\n\n      // Insert dataset\n      this.db.run(`\n        INSERT INTO data_datasets (id, file_path, format, row_count, column_count, file_size, content_hash, summary, indexed_at, metadata_json)\n        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n      `, [datasetId, relPath, parser.name, totalRows, columns.length, stat.size, contentHash, null, Date.now(), metadataJson ?? null]);\n\n      // Insert column profiles\n      for (const col of columnProfiles) {\n        this.db.run(`\n          INSERT INTO data_columns (id, dataset_id, name, position, inferred_type, nullable, null_count, null_pct, cardinality, min_value, max_value, mean_value, sample_values, summary, updated_at)\n          VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n        `, [\n          col.id, col.datasetId, col.name, col.position, col.inferredType,\n          col.nullable ? 1 : 0, col.nullCount, col.nullPct, col.cardinality,\n          col.minValue, col.maxValue, col.meanValue,\n          JSON.stringify(col.sampleValues), col.summary, col.updatedAt,\n        ]);\n      }\n\n      // Create row table with dynamic schema\n      const colDefs = columns.map(c => `\"${c.replace(/\"/g, '\"\"')}\" TEXT`).join(', ');\n      this.db.run(`CREATE TABLE \"${rowTableName}\" (rowid INTEGER PRIMARY KEY AUTOINCREMENT, ${colDefs})`);\n\n      // Insert rows in batches\n      const colNames = columns.map(c => `\"${c.replace(/\"/g, '\"\"')}\"`).join(', ');\n      const placeholders = columns.map(() => '?').join(', ');\n      const insertStmt = `INSERT INTO \"${rowTableName}\" (${colNames}) VALUES (${placeholders})`;\n\n      for (const row of allRows) {\n        const values = columns.map(c => {\n          const v = row[c];\n          if (v === null || v === undefined) return null;\n          if (typeof v === 'object') return JSON.stringify(v);\n          return v;\n        });\n        this.db.run(insertStmt, values);\n      }\n\n      // Save history snapshot for drift detection\n      const historyColumns = columnProfiles.map(col => ({\n        name: col.name,\n        type: col.inferredType,\n        cardinality: col.cardinality,\n        nullPct: col.nullPct,\n      }));\n      this.db.run(`\n        INSERT INTO data_dataset_history (dataset_id, snapshot_at, row_count, column_count, columns_json, content_hash)\n        VALUES (?, ?, ?, ?, ?, ?)\n      `, [datasetId, Date.now(), totalRows, columns.length, JSON.stringify(historyColumns), contentHash]);\n\n      this.db.run('COMMIT');\n    } catch (err) {\n      this.db.run('ROLLBACK');\n      throw err;\n    }\n\n    return { rows: totalRows, columns: columns.length };\n  }\n\n  // \u2500\u2500 Private \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\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n  private scanDataFiles(): string[] {\n    const includePatterns = (this.config as any).dataInclude ?? [];\n    const excludePatterns = (this.config as any).dataExclude ?? [];\n    const includeMatchers = includePatterns.map((p: string) => picomatch(p));\n    const excludeMatchers = excludePatterns.map((p: string) => picomatch(p));\n    const results: string[] = [];\n\n    const walk = (dir: string) => {\n      let entries: fs.Dirent[];\n      try { entries = fs.readdirSync(dir, { withFileTypes: true }); } catch { return; }\n\n      for (const entry of entries) {\n        const full = path.join(dir, entry.name);\n        const rel = path.relative(this.projectRoot, full).replace(/\\\\/g, '/');\n\n        if (entry.isDirectory()) {\n          if (excludeMatchers.some((m: any) => m(rel + '/'))) continue;\n          walk(full);\n        } else if (entry.isFile()) {\n          if (excludeMatchers.some((m: any) => m(rel))) continue;\n          if (includeMatchers.some((m: any) => m(rel))) {\n            // Verify a parser exists for this format\n            if (getDataParser(rel)) {\n              results.push(rel);\n            }\n          }\n        }\n      }\n    };\n\n    walk(this.projectRoot);\n    return results;\n  }\n\n  private removeDeletedDatasets(currentFiles: string[]): void {\n    const currentSet = new Set(currentFiles.map(f => generateDatasetId(f)));\n    const indexed = (this.db.all('SELECT id FROM data_datasets') as Array<{ id: string }>).map(r => r.id);\n\n    for (const id of indexed) {\n      if (!currentSet.has(id)) {\n        const rowTableName = `data_rows_${id.replace(/[^a-zA-Z0-9_]/g, '_')}`;\n        this.db.run(`DROP TABLE IF EXISTS \"${rowTableName}\"`);\n        this.db.run('DELETE FROM data_columns WHERE dataset_id = ?', [id]);\n        this.db.run('DELETE FROM data_code_refs WHERE dataset_id = ?', [id]);\n        this.db.run('DELETE FROM data_datasets WHERE id = ?', [id]);\n      }\n    }\n  }\n}\n"],
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   "names": ["picomatch"]
 }

package/dist/data/linker.js

@@ -33,13 +33,17 @@ const READ_PATTERNS = [
   /read_json\s*\(\s*['"`]([^'"`]+)['"`]/g,
   /read_parquet\s*\(\s*['"`]([^'"`]+)['"`]/g,
   /read_table\s*\(\s*['"`]([^'"`]+)['"`]/g,
-  // Python open
-  /open\s*\(\s*['"`]([^'"`]+\.(?:csv|tsv|jsonl|ndjson|json|xlsx|xls|parquet))['"`]/g,
+  // Python open (includes PDF)
+  /open\s*\(\s*['"`]([^'"`]+\.(?:csv|tsv|jsonl|ndjson|json|xlsx|xls|parquet|pdf))['"`]/g,
+  // Python PDF libraries
+  /PdfReader\s*\(\s*['"`]([^'"`]+\.pdf)['"`]/g,
+  /pdfplumber\.open\s*\(\s*['"`]([^'"`]+\.pdf)['"`]/g,
+  /fitz\.open\s*\(\s*['"`]([^'"`]+\.pdf)['"`]/g,
   // SQL COPY
   /COPY\s+\w+\s+FROM\s+['"`]([^'"`]+)['"`]/gi,
   /\\copy\s+\w+\s+from\s+['"`]([^'"`]+)['"`]/gi,
   // Generic path references in strings (data file extensions)
-  /['"`]((?:\.\.?\/)?(?:[\w\-./]+\/)?[\w\-]+\.(?:csv|tsv|jsonl|ndjson|xlsx|xls|parquet))['"`]/g
+  /['"`]((?:\.\.?\/)?(?:[\w\-./]+\/)?[\w\-]+\.(?:csv|tsv|jsonl|ndjson|xlsx|xls|parquet|pdf))['"`]/g
 ];
 const WRITE_PATTERNS = [
   /writeFileSync\s*\(\s*['"`]([^'"`]+\.(?:csv|tsv|jsonl|json|xlsx|parquet))['"`]/g,
@@ -92,7 +96,7 @@ function normalizePath(p) {
 function isDataFilePath(filePath, knownPaths) {
   if (knownPaths.has(filePath)) return true;
   const ext = filePath.split(".").pop()?.toLowerCase();
-  return ["csv", "tsv", "jsonl", "ndjson", "json", "xlsx", "xls", "parquet"].includes(ext ?? "");
+  return ["csv", "tsv", "jsonl", "ndjson", "json", "xlsx", "xls", "parquet", "pdf"].includes(ext ?? "");
 }
 class DataCodeLinker {
   constructor(db, projectRoot) {
@@ -111,7 +115,7 @@ class DataCodeLinker {
     const knownPaths = new Set(datasets.map((d) => d.file_path));
     const pathToDatasetId = new Map(datasets.map((d) => [d.file_path, d.id]));
     const sourceFiles = this.db.all(
-      `SELECT file_path FROM files WHERE file_path NOT LIKE '%.csv' AND file_path NOT LIKE '%.tsv' AND file_path NOT LIKE '%.jsonl' AND file_path NOT LIKE '%.ndjson' AND file_path NOT LIKE '%.xlsx' AND file_path NOT LIKE '%.parquet'`
+      `SELECT path AS file_path FROM files WHERE path NOT LIKE '%.csv' AND path NOT LIKE '%.tsv' AND path NOT LIKE '%.jsonl' AND path NOT LIKE '%.ndjson' AND path NOT LIKE '%.xlsx' AND path NOT LIKE '%.parquet' AND path NOT LIKE '%.pdf'`
     );
     this.db.run("DELETE FROM data_code_refs");
     let refsCreated = 0;

package/dist/data/linker.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/data/linker.ts"],
-  "sourcesContent": ["/**\n * Data \u2194 Code Linker\n *\n * Detects references to data files in source code and populates data_code_refs.\n * Patterns detected:\n *   - readFileSync('data/users.csv'), readFile('path/to/file.csv')\n *   - pd.read_csv('data/file.csv'), pd.read_excel(...)\n *   - open('data/file.csv'), csv.reader(open(...))\n *   - COPY FROM 'file.csv', \\copy ... from 'file.csv'\n *   - require('./data/file.json'), import ... from './data/file.json'\n *   - fs.createReadStream('data/file.csv')\n *   - String literals matching known data file paths\n */\n\nimport type { DataCodeRef } from './types';\n\n/** Patterns that indicate a code symbol reads a data file */\nconst READ_PATTERNS = [\n  // Node.js / TypeScript\n  /readFileSync\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /readFile\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /createReadStream\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  // Python pandas\n  /read_csv\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /read_excel\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /read_json\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /read_parquet\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /read_table\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  // Python open\n  /open\\s*\\(\\s*['\"`]([^'\"`]+\\.(?:csv|tsv|jsonl|ndjson|json|xlsx|xls|parquet))['\"`]/g,\n  // SQL COPY\n  /COPY\\s+\\w+\\s+FROM\\s+['\"`]([^'\"`]+)['\"`]/gi,\n  /\\\\copy\\s+\\w+\\s+from\\s+['\"`]([^'\"`]+)['\"`]/gi,\n  // Generic path references in strings (data file extensions)\n  /['\"`]((?:\\.\\.?\\/)?(?:[\\w\\-./]+\\/)?[\\w\\-]+\\.(?:csv|tsv|jsonl|ndjson|xlsx|xls|parquet))['\"`]/g,\n];\n\n/** Patterns that indicate a code symbol writes a data file */\nconst WRITE_PATTERNS = [\n  /writeFileSync\\s*\\(\\s*['\"`]([^'\"`]+\\.(?:csv|tsv|jsonl|json|xlsx|parquet))['\"`]/g,\n  /writeFile\\s*\\(\\s*['\"`]([^'\"`]+\\.(?:csv|tsv|jsonl|json|xlsx|parquet))['\"`]/g,\n  /to_csv\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /to_excel\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /to_json\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /to_parquet\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /createWriteStream\\s*\\(\\s*['\"`]([^'\"`]+\\.(?:csv|tsv|jsonl|json|xlsx|parquet))['\"`]/g,\n  /COPY\\s+\\w+\\s+TO\\s+['\"`]([^'\"`]+)['\"`]/gi,\n];\n\n/**\n * Scan source code content for references to data files.\n * Returns matched file paths with their reference type.\n */\nexport function detectDataReferences(\n  sourceContent: string,\n  knownDataPaths: Set<string>,\n): Array<{ filePath: string; refType: 'reads' | 'writes'; confidence: number }> {\n  const refs = new Map<string, { refType: 'reads' | 'writes'; confidence: number }>();\n\n  // Check read patterns\n  for (const pattern of READ_PATTERNS) {\n    pattern.lastIndex = 0;\n    let match: RegExpExecArray | null;\n    while ((match = pattern.exec(sourceContent)) !== null) {\n      const filePath = normalizePath(match[1]!);\n      if (isDataFilePath(filePath, knownDataPaths)) {\n        const existing = refs.get(filePath);\n        if (!existing || existing.confidence < 0.9) {\n          const confidence = knownDataPaths.has(filePath) ? 1.0 : 0.7;\n          refs.set(filePath, { refType: 'reads', confidence });\n        }\n      }\n    }\n  }\n\n  // Check write patterns\n  for (const pattern of WRITE_PATTERNS) {\n    pattern.lastIndex = 0;\n    let match: RegExpExecArray | null;\n    while ((match = pattern.exec(sourceContent)) !== null) {\n      const filePath = normalizePath(match[1]!);\n      if (isDataFilePath(filePath, knownDataPaths)) {\n        const confidence = knownDataPaths.has(filePath) ? 1.0 : 0.7;\n        refs.set(filePath, { refType: 'writes', confidence });\n      }\n    }\n  }\n\n  return Array.from(refs.entries()).map(([filePath, info]) => ({\n    filePath,\n    ...info,\n  }));\n}\n\n/**\n * Generate dataset ID from a file path (same logic as indexer).\n */\nfunction generateDatasetId(filePath: string): string {\n  return filePath\n    .replace(/\\.[^.]+$/, '')\n    .replace(/[/\\\\]/g, '-')\n    .replace(/[^a-zA-Z0-9-_]/g, '-')\n    .replace(/-+/g, '-')\n    .replace(/^-|-$/g, '')\n    .toLowerCase();\n}\n\n/**\n * Normalize a path reference found in code.\n * Strips leading ./ and resolves simple relative paths.\n */\nfunction normalizePath(p: string): string {\n  return p.replace(/^\\.\\//, '').replace(/\\\\/g, '/');\n}\n\n/**\n * Check if a path looks like a data file (by extension or known path match).\n */\nfunction isDataFilePath(filePath: string, knownPaths: Set<string>): boolean {\n  if (knownPaths.has(filePath)) return true;\n  // Check extension\n  const ext = filePath.split('.').pop()?.toLowerCase();\n  return ['csv', 'tsv', 'jsonl', 'ndjson', 'json', 'xlsx', 'xls', 'parquet'].includes(ext ?? '');\n}\n\n/**\n * Link data files to code symbols.\n * Scans all indexed source files for references to known data file paths.\n */\nexport class DataCodeLinker {\n  private readonly db: any;\n  private readonly projectRoot: string;\n\n  constructor(db: any, projectRoot: string) {\n    this.db = db;\n    this.projectRoot = projectRoot;\n  }\n\n  /**\n   * Populate data_code_refs by scanning source files for data file references.\n   * Returns the number of refs created.\n   */\n  linkAll(): number {\n    const fs = require('fs');\n    const path = require('path');\n\n    // Get all known data file paths\n    const datasets = this.db.all('SELECT id, file_path FROM data_datasets') as Array<{ id: string; file_path: string }>;\n    if (datasets.length === 0) return 0;\n\n    const knownPaths = new Set(datasets.map(d => d.file_path));\n    const pathToDatasetId = new Map(datasets.map(d => [d.file_path, d.id]));\n\n    // Get all indexed source files (from the graph)\n    const sourceFiles = this.db.all(\n      `SELECT file_path FROM files WHERE file_path NOT LIKE '%.csv' AND file_path NOT LIKE '%.tsv' AND file_path NOT LIKE '%.jsonl' AND file_path NOT LIKE '%.ndjson' AND file_path NOT LIKE '%.xlsx' AND file_path NOT LIKE '%.parquet'`\n    ) as Array<{ file_path: string }>;\n\n    // Clear existing refs\n    this.db.run('DELETE FROM data_code_refs');\n\n    let refsCreated = 0;\n\n    for (const file of sourceFiles) {\n      const absPath = path.join(this.projectRoot, file.file_path);\n      let content: string;\n      try {\n        content = fs.readFileSync(absPath, 'utf-8');\n      } catch {\n        continue;\n      }\n\n      const refs = detectDataReferences(content, knownPaths);\n      if (refs.length === 0) continue;\n\n      // Find the qualified_name of the containing symbol (file-level)\n      // Use the file path as the qualified name for file-level refs\n      const qualifiedName = file.file_path;\n\n      for (const ref of refs) {\n        const datasetId = pathToDatasetId.get(ref.filePath);\n        if (!datasetId) continue;\n\n        try {\n          this.db.run(\n            `INSERT OR REPLACE INTO data_code_refs (dataset_id, qualified_name, ref_type, confidence) VALUES (?, ?, ?, ?)`,\n            [datasetId, qualifiedName, ref.refType, ref.confidence],\n          );\n          refsCreated++;\n        } catch {\n          // Ignore duplicates\n        }\n      }\n    }\n\n    return refsCreated;\n  }\n}\n"],
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+  "sourcesContent": ["/**\n * Data \u2194 Code Linker\n *\n * Detects references to data files in source code and populates data_code_refs.\n * Patterns detected:\n *   - readFileSync('data/users.csv'), readFile('path/to/file.csv')\n *   - pd.read_csv('data/file.csv'), pd.read_excel(...)\n *   - open('data/file.csv'), csv.reader(open(...))\n *   - COPY FROM 'file.csv', \\copy ... from 'file.csv'\n *   - require('./data/file.json'), import ... from './data/file.json'\n *   - fs.createReadStream('data/file.csv')\n *   - String literals matching known data file paths\n */\n\nimport type { DataCodeRef } from './types';\n\n/** Patterns that indicate a code symbol reads a data file */\nconst READ_PATTERNS = [\n  // Node.js / TypeScript\n  /readFileSync\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /readFile\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /createReadStream\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  // Python pandas\n  /read_csv\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /read_excel\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /read_json\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /read_parquet\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /read_table\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  // Python open (includes PDF)\n  /open\\s*\\(\\s*['\"`]([^'\"`]+\\.(?:csv|tsv|jsonl|ndjson|json|xlsx|xls|parquet|pdf))['\"`]/g,\n  // Python PDF libraries\n  /PdfReader\\s*\\(\\s*['\"`]([^'\"`]+\\.pdf)['\"`]/g,\n  /pdfplumber\\.open\\s*\\(\\s*['\"`]([^'\"`]+\\.pdf)['\"`]/g,\n  /fitz\\.open\\s*\\(\\s*['\"`]([^'\"`]+\\.pdf)['\"`]/g,\n  // SQL COPY\n  /COPY\\s+\\w+\\s+FROM\\s+['\"`]([^'\"`]+)['\"`]/gi,\n  /\\\\copy\\s+\\w+\\s+from\\s+['\"`]([^'\"`]+)['\"`]/gi,\n  // Generic path references in strings (data file extensions)\n  /['\"`]((?:\\.\\.?\\/)?(?:[\\w\\-./]+\\/)?[\\w\\-]+\\.(?:csv|tsv|jsonl|ndjson|xlsx|xls|parquet|pdf))['\"`]/g,\n];\n\n/** Patterns that indicate a code symbol writes a data file */\nconst WRITE_PATTERNS = [\n  /writeFileSync\\s*\\(\\s*['\"`]([^'\"`]+\\.(?:csv|tsv|jsonl|json|xlsx|parquet))['\"`]/g,\n  /writeFile\\s*\\(\\s*['\"`]([^'\"`]+\\.(?:csv|tsv|jsonl|json|xlsx|parquet))['\"`]/g,\n  /to_csv\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /to_excel\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /to_json\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /to_parquet\\s*\\(\\s*['\"`]([^'\"`]+)['\"`]/g,\n  /createWriteStream\\s*\\(\\s*['\"`]([^'\"`]+\\.(?:csv|tsv|jsonl|json|xlsx|parquet))['\"`]/g,\n  /COPY\\s+\\w+\\s+TO\\s+['\"`]([^'\"`]+)['\"`]/gi,\n];\n\n/**\n * Scan source code content for references to data files.\n * Returns matched file paths with their reference type.\n */\nexport function detectDataReferences(\n  sourceContent: string,\n  knownDataPaths: Set<string>,\n): Array<{ filePath: string; refType: 'reads' | 'writes'; confidence: number }> {\n  const refs = new Map<string, { refType: 'reads' | 'writes'; confidence: number }>();\n\n  // Check read patterns\n  for (const pattern of READ_PATTERNS) {\n    pattern.lastIndex = 0;\n    let match: RegExpExecArray | null;\n    while ((match = pattern.exec(sourceContent)) !== null) {\n      const filePath = normalizePath(match[1]!);\n      if (isDataFilePath(filePath, knownDataPaths)) {\n        const existing = refs.get(filePath);\n        if (!existing || existing.confidence < 0.9) {\n          const confidence = knownDataPaths.has(filePath) ? 1.0 : 0.7;\n          refs.set(filePath, { refType: 'reads', confidence });\n        }\n      }\n    }\n  }\n\n  // Check write patterns\n  for (const pattern of WRITE_PATTERNS) {\n    pattern.lastIndex = 0;\n    let match: RegExpExecArray | null;\n    while ((match = pattern.exec(sourceContent)) !== null) {\n      const filePath = normalizePath(match[1]!);\n      if (isDataFilePath(filePath, knownDataPaths)) {\n        const confidence = knownDataPaths.has(filePath) ? 1.0 : 0.7;\n        refs.set(filePath, { refType: 'writes', confidence });\n      }\n    }\n  }\n\n  return Array.from(refs.entries()).map(([filePath, info]) => ({\n    filePath,\n    ...info,\n  }));\n}\n\n/**\n * Generate dataset ID from a file path (same logic as indexer).\n */\nfunction generateDatasetId(filePath: string): string {\n  return filePath\n    .replace(/\\.[^.]+$/, '')\n    .replace(/[/\\\\]/g, '-')\n    .replace(/[^a-zA-Z0-9-_]/g, '-')\n    .replace(/-+/g, '-')\n    .replace(/^-|-$/g, '')\n    .toLowerCase();\n}\n\n/**\n * Normalize a path reference found in code.\n * Strips leading ./ and resolves simple relative paths.\n */\nfunction normalizePath(p: string): string {\n  return p.replace(/^\\.\\//, '').replace(/\\\\/g, '/');\n}\n\n/**\n * Check if a path looks like a data file (by extension or known path match).\n */\nfunction isDataFilePath(filePath: string, knownPaths: Set<string>): boolean {\n  if (knownPaths.has(filePath)) return true;\n  // Check extension\n  const ext = filePath.split('.').pop()?.toLowerCase();\n  return ['csv', 'tsv', 'jsonl', 'ndjson', 'json', 'xlsx', 'xls', 'parquet', 'pdf'].includes(ext ?? '');\n}\n\n/**\n * Link data files to code symbols.\n * Scans all indexed source files for references to known data file paths.\n */\nexport class DataCodeLinker {\n  private readonly db: any;\n  private readonly projectRoot: string;\n\n  constructor(db: any, projectRoot: string) {\n    this.db = db;\n    this.projectRoot = projectRoot;\n  }\n\n  /**\n   * Populate data_code_refs by scanning source files for data file references.\n   * Returns the number of refs created.\n   */\n  linkAll(): number {\n    const fs = require('fs');\n    const path = require('path');\n\n    // Get all known data file paths\n    const datasets = this.db.all('SELECT id, file_path FROM data_datasets') as Array<{ id: string; file_path: string }>;\n    if (datasets.length === 0) return 0;\n\n    const knownPaths = new Set(datasets.map(d => d.file_path));\n    const pathToDatasetId = new Map(datasets.map(d => [d.file_path, d.id]));\n\n    // Get all indexed source files (from the graph)\n    // Note: files table uses 'path' as the column name, aliased to file_path for readability.\n    const sourceFiles = this.db.all(\n      `SELECT path AS file_path FROM files WHERE path NOT LIKE '%.csv' AND path NOT LIKE '%.tsv' AND path NOT LIKE '%.jsonl' AND path NOT LIKE '%.ndjson' AND path NOT LIKE '%.xlsx' AND path NOT LIKE '%.parquet' AND path NOT LIKE '%.pdf'`\n    ) as Array<{ file_path: string }>;\n\n    // Clear existing refs\n    this.db.run('DELETE FROM data_code_refs');\n\n    let refsCreated = 0;\n\n    for (const file of sourceFiles) {\n      const absPath = path.join(this.projectRoot, file.file_path);\n      let content: string;\n      try {\n        content = fs.readFileSync(absPath, 'utf-8');\n      } catch {\n        continue;\n      }\n\n      const refs = detectDataReferences(content, knownPaths);\n      if (refs.length === 0) continue;\n\n      // Find the qualified_name of the containing symbol (file-level)\n      // Use the file path as the qualified name for file-level refs\n      const qualifiedName = file.file_path;\n\n      for (const ref of refs) {\n        const datasetId = pathToDatasetId.get(ref.filePath);\n        if (!datasetId) continue;\n\n        try {\n          this.db.run(\n            `INSERT OR REPLACE INTO data_code_refs (dataset_id, qualified_name, ref_type, confidence) VALUES (?, ?, ?, ?)`,\n            [datasetId, qualifiedName, ref.refType, ref.confidence],\n          );\n          refsCreated++;\n        } catch {\n          // Ignore duplicates\n        }\n      }\n    }\n\n    return refsCreated;\n  }\n}\n"],
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   "names": []
 }

package/dist/data/linker.test.js

@@ -0,0 +1,60 @@
+"use strict";
+var import_vitest = require("vitest");
+var import_linker = require("./linker");
+const KNOWN_PATHS = /* @__PURE__ */ new Set([
+  "data/report.pdf",
+  "docs/manual.pdf",
+  "data/users.csv"
+]);
+(0, import_vitest.describe)("detectDataReferences \u2014 PDF patterns", () => {
+  (0, import_vitest.it)("detects readFileSync with .pdf path", () => {
+    const src = `const buf = readFileSync('data/report.pdf')`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath === "data/report.pdf" && r.refType === "reads")).toBe(true);
+  });
+  (0, import_vitest.it)("detects createReadStream with .pdf path", () => {
+    const src = `fs.createReadStream('data/report.pdf')`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath === "data/report.pdf")).toBe(true);
+  });
+  (0, import_vitest.it)("detects Python open() with .pdf extension", () => {
+    const src = `f = open('docs/manual.pdf', 'rb')`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath === "docs/manual.pdf")).toBe(true);
+  });
+  (0, import_vitest.it)("detects PdfReader() call", () => {
+    const src = `reader = PdfReader('data/report.pdf')`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath === "data/report.pdf")).toBe(true);
+  });
+  (0, import_vitest.it)("detects pdfplumber.open() call", () => {
+    const src = `with pdfplumber.open('data/report.pdf') as pdf:`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath === "data/report.pdf")).toBe(true);
+  });
+  (0, import_vitest.it)("detects fitz.open() call", () => {
+    const src = `doc = fitz.open('docs/manual.pdf')`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath === "docs/manual.pdf")).toBe(true);
+  });
+  (0, import_vitest.it)("detects generic string literal with .pdf extension", () => {
+    const src = `const path = 'data/report.pdf';`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath === "data/report.pdf")).toBe(true);
+  });
+  (0, import_vitest.it)("gives confidence 1.0 for known paths, lower for unknown", () => {
+    const src = `readFileSync('data/report.pdf'); readFileSync('other/unknown.pdf')`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    const known = refs.find((r) => r.filePath === "data/report.pdf");
+    const unknown = refs.find((r) => r.filePath === "other/unknown.pdf");
+    (0, import_vitest.expect)(known?.confidence).toBe(1);
+    (0, import_vitest.expect)(unknown?.confidence).toBeLessThan(1);
+  });
+  (0, import_vitest.it)("does not confuse .pdf with .csv patterns", () => {
+    const src = `readFileSync('data/users.csv')`;
+    const refs = (0, import_linker.detectDataReferences)(src, KNOWN_PATHS);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath === "data/users.csv")).toBe(true);
+    (0, import_vitest.expect)(refs.some((r) => r.filePath?.endsWith(".pdf"))).toBe(false);
+  });
+});
+//# sourceMappingURL=linker.test.js.map

package/dist/data/linker.test.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/data/linker.test.ts"],
+  "sourcesContent": ["import { describe, it, expect } from 'vitest';\nimport { detectDataReferences } from './linker';\n\nconst KNOWN_PATHS = new Set([\n  'data/report.pdf',\n  'docs/manual.pdf',\n  'data/users.csv',\n]);\n\ndescribe('detectDataReferences \u2014 PDF patterns', () => {\n  it('detects readFileSync with .pdf path', () => {\n    const src = `const buf = readFileSync('data/report.pdf')`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    expect(refs.some(r => r.filePath === 'data/report.pdf' && r.refType === 'reads')).toBe(true);\n  });\n\n  it('detects createReadStream with .pdf path', () => {\n    const src = `fs.createReadStream('data/report.pdf')`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    expect(refs.some(r => r.filePath === 'data/report.pdf')).toBe(true);\n  });\n\n  it('detects Python open() with .pdf extension', () => {\n    const src = `f = open('docs/manual.pdf', 'rb')`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    expect(refs.some(r => r.filePath === 'docs/manual.pdf')).toBe(true);\n  });\n\n  it('detects PdfReader() call', () => {\n    const src = `reader = PdfReader('data/report.pdf')`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    expect(refs.some(r => r.filePath === 'data/report.pdf')).toBe(true);\n  });\n\n  it('detects pdfplumber.open() call', () => {\n    const src = `with pdfplumber.open('data/report.pdf') as pdf:`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    expect(refs.some(r => r.filePath === 'data/report.pdf')).toBe(true);\n  });\n\n  it('detects fitz.open() call', () => {\n    const src = `doc = fitz.open('docs/manual.pdf')`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    expect(refs.some(r => r.filePath === 'docs/manual.pdf')).toBe(true);\n  });\n\n  it('detects generic string literal with .pdf extension', () => {\n    const src = `const path = 'data/report.pdf';`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    expect(refs.some(r => r.filePath === 'data/report.pdf')).toBe(true);\n  });\n\n  it('gives confidence 1.0 for known paths, lower for unknown', () => {\n    const src = `readFileSync('data/report.pdf'); readFileSync('other/unknown.pdf')`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    const known = refs.find(r => r.filePath === 'data/report.pdf');\n    const unknown = refs.find(r => r.filePath === 'other/unknown.pdf');\n    expect(known?.confidence).toBe(1.0);\n    expect(unknown?.confidence).toBeLessThan(1.0);\n  });\n\n  it('does not confuse .pdf with .csv patterns', () => {\n    const src = `readFileSync('data/users.csv')`;\n    const refs = detectDataReferences(src, KNOWN_PATHS);\n    expect(refs.some(r => r.filePath === 'data/users.csv')).toBe(true);\n    expect(refs.some(r => r.filePath?.endsWith('.pdf'))).toBe(false);\n  });\n});\n"],
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+  "names": []
+}

package/dist/data/parsers/__fixtures__/pdf-inspector-stub.js

@@ -0,0 +1,41 @@
+"use strict";
+var __defProp = Object.defineProperty;
+var __getOwnPropDesc = Object.getOwnPropertyDescriptor;
+var __getOwnPropNames = Object.getOwnPropertyNames;
+var __hasOwnProp = Object.prototype.hasOwnProperty;
+var __export = (target, all) => {
+  for (var name in all)
+    __defProp(target, name, { get: all[name], enumerable: true });
+};
+var __copyProps = (to, from, except, desc) => {
+  if (from && typeof from === "object" || typeof from === "function") {
+    for (let key of __getOwnPropNames(from))
+      if (!__hasOwnProp.call(to, key) && key !== except)
+        __defProp(to, key, { get: () => from[key], enumerable: !(desc = __getOwnPropDesc(from, key)) || desc.enumerable });
+  }
+  return to;
+};
+var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: true }), mod);
+var pdf_inspector_stub_exports = {};
+__export(pdf_inspector_stub_exports, {
+  classifyPdf: () => classifyPdf,
+  extractPagesMarkdown: () => extractPagesMarkdown,
+  processPdf: () => processPdf
+});
+module.exports = __toCommonJS(pdf_inspector_stub_exports);
+function extractPagesMarkdown(_buf) {
+  throw new Error("@firecrawl/pdf-inspector is not installed");
+}
+function processPdf(_buf) {
+  throw new Error("@firecrawl/pdf-inspector is not installed");
+}
+function classifyPdf(_buf) {
+  throw new Error("@firecrawl/pdf-inspector is not installed");
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  classifyPdf,
+  extractPagesMarkdown,
+  processPdf
+});
+//# sourceMappingURL=pdf-inspector-stub.js.map

package/dist/data/parsers/__fixtures__/pdf-inspector-stub.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../../../src/data/parsers/__fixtures__/pdf-inspector-stub.ts"],
+  "sourcesContent": ["// Stub for @firecrawl/pdf-inspector used in tests.\n// Real package not installed \u2014 this stub allows require() to resolve.\n// vi.mock('@firecrawl/pdf-inspector', factory) overrides this in individual tests.\nexport function extractPagesMarkdown(_buf: Buffer): never {\n  throw new Error('@firecrawl/pdf-inspector is not installed');\n}\nexport function processPdf(_buf: Buffer): never {\n  throw new Error('@firecrawl/pdf-inspector is not installed');\n}\nexport function classifyPdf(_buf: Buffer): never {\n  throw new Error('@firecrawl/pdf-inspector is not installed');\n}\n"],
+  "mappings": ";;;;;;;;;;;;;;;;;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAGO,SAAS,qBAAqB,MAAqB;AACxD,QAAM,IAAI,MAAM,2CAA2C;AAC7D;AACO,SAAS,WAAW,MAAqB;AAC9C,QAAM,IAAI,MAAM,2CAA2C;AAC7D;AACO,SAAS,YAAY,MAAqB;AAC/C,QAAM,IAAI,MAAM,2CAA2C;AAC7D;",
+  "names": []
+}

package/dist/data/parsers/index.js

@@ -29,13 +29,15 @@ var import_jsonl = require("./jsonl");
 var import_json_array = require("./json-array");
 var import_excel = require("./excel");
 var import_parquet = require("./parquet");
+var import_pdf = require("./pdf");
 const allParsers = [
   import_csv.csvParser,
   import_csv.tsvParser,
   import_jsonl.jsonlParser,
   import_json_array.jsonArrayParser,
   import_excel.excelParser,
-  import_parquet.parquetParser
+  import_parquet.parquetParser,
+  import_pdf.pdfParser
 ];
 const extensionMap = /* @__PURE__ */ new Map();
 for (const parser of allParsers) {

package/dist/data/parsers/index.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../src/data/parsers/index.ts"],
-  "sourcesContent": ["/**\n * Data Format Registry\n *\n * Maps file extensions to their appropriate parser.\n * Gracefully skips formats whose optional dependencies are not installed.\n */\n\nimport type { DataFormatParser } from '../types';\nimport { csvParser, tsvParser } from './csv';\nimport { jsonlParser } from './jsonl';\nimport { jsonArrayParser } from './json-array';\nimport { excelParser } from './excel';\nimport { parquetParser } from './parquet';\n\n// \u2500\u2500 Registry \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\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nconst allParsers: DataFormatParser[] = [\n  csvParser,\n  tsvParser,\n  jsonlParser,\n  jsonArrayParser,\n  excelParser,\n  parquetParser,\n];\n\n/** Extension \u2192 parser lookup */\nconst extensionMap = new Map<string, DataFormatParser>();\nfor (const parser of allParsers) {\n  for (const ext of parser.extensions) {\n    extensionMap.set(ext.toLowerCase(), parser);\n  }\n}\n\n// \u2500\u2500 Public API \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\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Get the parser for a given file extension.\n * Returns null if no parser is registered or the optional dep is missing.\n */\nexport function getDataParser(filePath: string): DataFormatParser | null {\n  const ext = filePath.slice(filePath.lastIndexOf('.')).toLowerCase();\n  const parser = extensionMap.get(ext) ?? null;\n  if (!parser) return null;\n  if (!parser.isAvailable()) return null;\n  return parser;\n}\n\n/**\n * Check if a file extension is supported for data parsing.\n */\nexport function isSupportedDataFormat(filePath: string): boolean {\n  return getDataParser(filePath) !== null;\n}\n\n/**\n * Get all supported extensions (only those with available deps).\n */\nexport function getAvailableExtensions(): string[] {\n  const available: string[] = [];\n  for (const [ext, parser] of extensionMap) {\n    if (parser.isAvailable()) available.push(ext);\n  }\n  return available;\n}\n\n/**\n * Get extensions that are registered but have missing optional deps.\n */\nexport function getUnavailableExtensions(): Array<{ ext: string; parser: string }> {\n  const unavailable: Array<{ ext: string; parser: string }> = [];\n  for (const [ext, parser] of extensionMap) {\n    if (!parser.isAvailable()) {\n      unavailable.push({ ext, parser: parser.name });\n    }\n  }\n  return unavailable;\n}\n"],
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+  "sourcesContent": ["/**\n * Data Format Registry\n *\n * Maps file extensions to their appropriate parser.\n * Gracefully skips formats whose optional dependencies are not installed.\n */\n\nimport type { DataFormatParser } from '../types';\nimport { csvParser, tsvParser } from './csv';\nimport { jsonlParser } from './jsonl';\nimport { jsonArrayParser } from './json-array';\nimport { excelParser } from './excel';\nimport { parquetParser } from './parquet';\nimport { pdfParser } from './pdf';\n\n// \u2500\u2500 Registry \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\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\nconst allParsers: DataFormatParser[] = [\n  csvParser,\n  tsvParser,\n  jsonlParser,\n  jsonArrayParser,\n  excelParser,\n  parquetParser,\n  pdfParser,\n];\n\n/** Extension \u2192 parser lookup */\nconst extensionMap = new Map<string, DataFormatParser>();\nfor (const parser of allParsers) {\n  for (const ext of parser.extensions) {\n    extensionMap.set(ext.toLowerCase(), parser);\n  }\n}\n\n// \u2500\u2500 Public API \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\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\n/**\n * Get the parser for a given file extension.\n * Returns null if no parser is registered or the optional dep is missing.\n */\nexport function getDataParser(filePath: string): DataFormatParser | null {\n  const ext = filePath.slice(filePath.lastIndexOf('.')).toLowerCase();\n  const parser = extensionMap.get(ext) ?? null;\n  if (!parser) return null;\n  if (!parser.isAvailable()) return null;\n  return parser;\n}\n\n/**\n * Check if a file extension is supported for data parsing.\n */\nexport function isSupportedDataFormat(filePath: string): boolean {\n  return getDataParser(filePath) !== null;\n}\n\n/**\n * Get all supported extensions (only those with available deps).\n */\nexport function getAvailableExtensions(): string[] {\n  const available: string[] = [];\n  for (const [ext, parser] of extensionMap) {\n    if (parser.isAvailable()) available.push(ext);\n  }\n  return available;\n}\n\n/**\n * Get extensions that are registered but have missing optional deps.\n */\nexport function getUnavailableExtensions(): Array<{ ext: string; parser: string }> {\n  const unavailable: Array<{ ext: string; parser: string }> = [];\n  for (const [ext, parser] of extensionMap) {\n    if (!parser.isAvailable()) {\n      unavailable.push({ ext, parser: parser.name });\n    }\n  }\n  return unavailable;\n}\n"],
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   "names": []
 }