kirograph 0.16.1 → 0.19.0

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)\n      if (this.config.enableArchitecture) {\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      // 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: 'architecture', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is non-critical */ }\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        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)\n      if (this.config.enableArchitecture) {\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      // 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: 'architecture', current: 0, total: 1, meta: { msg } }),\n          });\n        } catch { /* docs indexing is 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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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      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        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      this.lock.clearDirty();\n      result.duration = Date.now() - start;\n      return result;\n    } finally {\n      this.lock.release();\n      release();\n    }\n  }\n}\n"],
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   "names": []
 }

package/dist/data/filters.js

@@ -0,0 +1,105 @@
+"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 filters_exports = {};
+__export(filters_exports, {
+  buildWhereClause: () => buildWhereClause
+});
+module.exports = __toCommonJS(filters_exports);
+function validateColumn(column, validColumns) {
+  if (!validColumns.has(column)) {
+    throw new Error(`Invalid column: "${column}". Available columns: ${[...validColumns].join(", ")}`);
+  }
+  return `"${column.replace(/"/g, '""')}"`;
+}
+function buildWhereClause(filters, validColumns) {
+  if (filters.length === 0) {
+    return { where: "", params: [] };
+  }
+  const conditions = [];
+  const params = [];
+  for (const filter of filters) {
+    const col = validateColumn(filter.column, validColumns);
+    switch (filter.op) {
+      case "eq":
+        conditions.push(`${col} = ?`);
+        params.push(filter.value);
+        break;
+      case "neq":
+        conditions.push(`${col} != ?`);
+        params.push(filter.value);
+        break;
+      case "gt":
+        conditions.push(`${col} > ?`);
+        params.push(filter.value);
+        break;
+      case "gte":
+        conditions.push(`${col} >= ?`);
+        params.push(filter.value);
+        break;
+      case "lt":
+        conditions.push(`${col} < ?`);
+        params.push(filter.value);
+        break;
+      case "lte":
+        conditions.push(`${col} <= ?`);
+        params.push(filter.value);
+        break;
+      case "contains":
+        conditions.push(`${col} LIKE ?`);
+        params.push(`%${filter.value}%`);
+        break;
+      case "in": {
+        if (!Array.isArray(filter.value) || filter.value.length === 0) {
+          conditions.push("0");
+        } else {
+          const placeholders = filter.value.map(() => "?").join(",");
+          conditions.push(`${col} IN (${placeholders})`);
+          params.push(...filter.value);
+        }
+        break;
+      }
+      case "is_null":
+        if (filter.value === true || filter.value === "true") {
+          conditions.push(`${col} IS NULL`);
+        } else {
+          conditions.push(`${col} IS NOT NULL`);
+        }
+        break;
+      case "between": {
+        if (!Array.isArray(filter.value) || filter.value.length !== 2) {
+          throw new Error(`"between" filter requires a [min, max] array`);
+        }
+        conditions.push(`${col} BETWEEN ? AND ?`);
+        params.push(filter.value[0], filter.value[1]);
+        break;
+      }
+      default:
+        throw new Error(`Unknown filter operator: "${filter.op}"`);
+    }
+  }
+  return {
+    where: `WHERE ${conditions.join(" AND ")}`,
+    params
+  };
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  buildWhereClause
+});
+//# sourceMappingURL=filters.js.map

package/dist/data/filters.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/data/filters.ts"],
+  "sourcesContent": ["/**\n * Structured Filter \u2192 SQL WHERE Clause Builder\n *\n * Converts QueryFilter objects into parameterized SQL.\n * Zero injection surface \u2014 column names are validated against schema,\n * values are always parameterized.\n */\n\nimport type { QueryFilter } from './types';\n\ninterface SQLClause {\n  where: string;\n  params: any[];\n}\n\n/**\n * Validate that a column name exists in the schema.\n * Prevents SQL injection via column names.\n */\nfunction validateColumn(column: string, validColumns: Set<string>): string {\n  if (!validColumns.has(column)) {\n    throw new Error(`Invalid column: \"${column}\". Available columns: ${[...validColumns].join(', ')}`);\n  }\n  // Quote column name to handle spaces and reserved words\n  return `\"${column.replace(/\"/g, '\"\"')}\"`;\n}\n\n/**\n * Build a parameterized WHERE clause from structured filters.\n * All filters are ANDed together.\n *\n * @param filters - Array of QueryFilter objects\n * @param validColumns - Set of valid column names (from schema)\n * @returns SQL WHERE clause and parameter array\n */\nexport function buildWhereClause(filters: QueryFilter[], validColumns: Set<string>): SQLClause {\n  if (filters.length === 0) {\n    return { where: '', params: [] };\n  }\n\n  const conditions: string[] = [];\n  const params: any[] = [];\n\n  for (const filter of filters) {\n    const col = validateColumn(filter.column, validColumns);\n\n    switch (filter.op) {\n      case 'eq':\n        conditions.push(`${col} = ?`);\n        params.push(filter.value);\n        break;\n\n      case 'neq':\n        conditions.push(`${col} != ?`);\n        params.push(filter.value);\n        break;\n\n      case 'gt':\n        conditions.push(`${col} > ?`);\n        params.push(filter.value);\n        break;\n\n      case 'gte':\n        conditions.push(`${col} >= ?`);\n        params.push(filter.value);\n        break;\n\n      case 'lt':\n        conditions.push(`${col} < ?`);\n        params.push(filter.value);\n        break;\n\n      case 'lte':\n        conditions.push(`${col} <= ?`);\n        params.push(filter.value);\n        break;\n\n      case 'contains':\n        conditions.push(`${col} LIKE ?`);\n        params.push(`%${filter.value}%`);\n        break;\n\n      case 'in': {\n        if (!Array.isArray(filter.value) || filter.value.length === 0) {\n          conditions.push('0'); // Always false\n        } else {\n          const placeholders = filter.value.map(() => '?').join(',');\n          conditions.push(`${col} IN (${placeholders})`);\n          params.push(...filter.value);\n        }\n        break;\n      }\n\n      case 'is_null':\n        if (filter.value === true || filter.value === 'true') {\n          conditions.push(`${col} IS NULL`);\n        } else {\n          conditions.push(`${col} IS NOT NULL`);\n        }\n        break;\n\n      case 'between': {\n        if (!Array.isArray(filter.value) || filter.value.length !== 2) {\n          throw new Error(`\"between\" filter requires a [min, max] array`);\n        }\n        conditions.push(`${col} BETWEEN ? AND ?`);\n        params.push(filter.value[0], filter.value[1]);\n        break;\n      }\n\n      default:\n        throw new Error(`Unknown filter operator: \"${(filter as any).op}\"`);\n    }\n  }\n\n  return {\n    where: `WHERE ${conditions.join(' AND ')}`,\n    params,\n  };\n}\n"],
+  "mappings": ";;;;;;;;;;;;;;;;;;AAAA;AAAA;AAAA;AAAA;AAAA;AAmBA,SAAS,eAAe,QAAgB,cAAmC;AACzE,MAAI,CAAC,aAAa,IAAI,MAAM,GAAG;AAC7B,UAAM,IAAI,MAAM,oBAAoB,MAAM,yBAAyB,CAAC,GAAG,YAAY,EAAE,KAAK,IAAI,CAAC,EAAE;AAAA,EACnG;AAEA,SAAO,IAAI,OAAO,QAAQ,MAAM,IAAI,CAAC;AACvC;AAUO,SAAS,iBAAiB,SAAwB,cAAsC;AAC7F,MAAI,QAAQ,WAAW,GAAG;AACxB,WAAO,EAAE,OAAO,IAAI,QAAQ,CAAC,EAAE;AAAA,EACjC;AAEA,QAAM,aAAuB,CAAC;AAC9B,QAAM,SAAgB,CAAC;AAEvB,aAAW,UAAU,SAAS;AAC5B,UAAM,MAAM,eAAe,OAAO,QAAQ,YAAY;AAEtD,YAAQ,OAAO,IAAI;AAAA,MACjB,KAAK;AACH,mBAAW,KAAK,GAAG,GAAG,MAAM;AAC5B,eAAO,KAAK,OAAO,KAAK;AACxB;AAAA,MAEF,KAAK;AACH,mBAAW,KAAK,GAAG,GAAG,OAAO;AAC7B,eAAO,KAAK,OAAO,KAAK;AACxB;AAAA,MAEF,KAAK;AACH,mBAAW,KAAK,GAAG,GAAG,MAAM;AAC5B,eAAO,KAAK,OAAO,KAAK;AACxB;AAAA,MAEF,KAAK;AACH,mBAAW,KAAK,GAAG,GAAG,OAAO;AAC7B,eAAO,KAAK,OAAO,KAAK;AACxB;AAAA,MAEF,KAAK;AACH,mBAAW,KAAK,GAAG,GAAG,MAAM;AAC5B,eAAO,KAAK,OAAO,KAAK;AACxB;AAAA,MAEF,KAAK;AACH,mBAAW,KAAK,GAAG,GAAG,OAAO;AAC7B,eAAO,KAAK,OAAO,KAAK;AACxB;AAAA,MAEF,KAAK;AACH,mBAAW,KAAK,GAAG,GAAG,SAAS;AAC/B,eAAO,KAAK,IAAI,OAAO,KAAK,GAAG;AAC/B;AAAA,MAEF,KAAK,MAAM;AACT,YAAI,CAAC,MAAM,QAAQ,OAAO,KAAK,KAAK,OAAO,MAAM,WAAW,GAAG;AAC7D,qBAAW,KAAK,GAAG;AAAA,QACrB,OAAO;AACL,gBAAM,eAAe,OAAO,MAAM,IAAI,MAAM,GAAG,EAAE,KAAK,GAAG;AACzD,qBAAW,KAAK,GAAG,GAAG,QAAQ,YAAY,GAAG;AAC7C,iBAAO,KAAK,GAAG,OAAO,KAAK;AAAA,QAC7B;AACA;AAAA,MACF;AAAA,MAEA,KAAK;AACH,YAAI,OAAO,UAAU,QAAQ,OAAO,UAAU,QAAQ;AACpD,qBAAW,KAAK,GAAG,GAAG,UAAU;AAAA,QAClC,OAAO;AACL,qBAAW,KAAK,GAAG,GAAG,cAAc;AAAA,QACtC;AACA;AAAA,MAEF,KAAK,WAAW;AACd,YAAI,CAAC,MAAM,QAAQ,OAAO,KAAK,KAAK,OAAO,MAAM,WAAW,GAAG;AAC7D,gBAAM,IAAI,MAAM,8CAA8C;AAAA,QAChE;AACA,mBAAW,KAAK,GAAG,GAAG,kBAAkB;AACxC,eAAO,KAAK,OAAO,MAAM,CAAC,GAAG,OAAO,MAAM,CAAC,CAAC;AAC5C;AAAA,MACF;AAAA,MAEA;AACE,cAAM,IAAI,MAAM,6BAA8B,OAAe,EAAE,GAAG;AAAA,IACtE;AAAA,EACF;AAEA,SAAO;AAAA,IACL,OAAO,SAAS,WAAW,KAAK,OAAO,CAAC;AAAA,IACxC;AAAA,EACF;AACF;",
+  "names": []
+}

package/dist/data/indexer.js

@@ -0,0 +1,225 @@
+"use strict";
+var __create = Object.create;
+var __defProp = Object.defineProperty;
+var __getOwnPropDesc = Object.getOwnPropertyDescriptor;
+var __getOwnPropNames = Object.getOwnPropertyNames;
+var __getProtoOf = Object.getPrototypeOf;
+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 __toESM = (mod, isNodeMode, target) => (target = mod != null ? __create(__getProtoOf(mod)) : {}, __copyProps(
+  // If the importer is in node compatibility mode or this is not an ESM
+  // file that has been converted to a CommonJS file using a Babel-
+  // compatible transform (i.e. "__esModule" has not been set), then set
+  // "default" to the CommonJS "module.exports" for node compatibility.
+  isNodeMode || !mod || !mod.__esModule ? __defProp(target, "default", { value: mod, enumerable: true }) : target,
+  mod
+));
+var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: true }), mod);
+var indexer_exports = {};
+__export(indexer_exports, {
+  DataIndexer: () => DataIndexer
+});
+module.exports = __toCommonJS(indexer_exports);
+var fs = __toESM(require("fs"));
+var path = __toESM(require("path"));
+var crypto = __toESM(require("crypto"));
+var import_picomatch = __toESM(require("picomatch"));
+var import_parsers = require("./parsers/index");
+var import_profiler = require("./profiler");
+function generateDatasetId(filePath) {
+  return filePath.replace(/\.[^.]+$/, "").replace(/[/\\]/g, "-").replace(/[^a-zA-Z0-9-_]/g, "-").replace(/-+/g, "-").replace(/^-|-$/g, "").toLowerCase();
+}
+class DataIndexer {
+  constructor(db, config, projectRoot) {
+    this.db = db;
+    this.config = config;
+    this.projectRoot = projectRoot;
+  }
+  async indexAll(opts) {
+    const start = Date.now();
+    const result = {
+      datasetsIndexed: 0,
+      rowsIndexed: 0,
+      columnsProfiled: 0,
+      errors: [],
+      duration: 0
+    };
+    const files = this.scanDataFiles();
+    opts?.onProgress?.(`data: found ${files.length} data files`);
+    for (const relPath of files) {
+      try {
+        const indexed = await this.indexFile(relPath, opts?.force ?? false);
+        if (indexed) {
+          result.datasetsIndexed++;
+          result.rowsIndexed += indexed.rows;
+          result.columnsProfiled += indexed.columns;
+        }
+      } catch (err) {
+        result.errors.push(`${relPath}: ${err instanceof Error ? err.message : String(err)}`);
+      }
+    }
+    this.removeDeletedDatasets(files);
+    if (this.config.dataLinkCode !== false && result.datasetsIndexed > 0) {
+      try {
+        const { DataCodeLinker } = await Promise.resolve().then(() => require("./linker.js"));
+        const linker = new DataCodeLinker(this.db, this.projectRoot);
+        const refsCreated = linker.linkAll();
+        opts?.onProgress?.(`data: linked ${refsCreated} code references`);
+      } catch {
+      }
+    }
+    result.duration = Date.now() - start;
+    return result;
+  }
+  async indexFile(relPath, force = false) {
+    const absPath = path.join(this.projectRoot, relPath);
+    if (!fs.existsSync(absPath)) return null;
+    const stat = fs.statSync(absPath);
+    if (stat.size > this.config.dataMaxFileSize) return null;
+    const fileBuffer = fs.readFileSync(absPath);
+    const contentHash = crypto.createHash("sha256").update(fileBuffer).digest("hex");
+    const datasetId = generateDatasetId(relPath);
+    if (!force) {
+      const existing = this.db.get("SELECT content_hash FROM data_datasets WHERE id = ?", [datasetId]);
+      if (existing?.content_hash === contentHash) return null;
+    }
+    const parser = (0, import_parsers.getDataParser)(relPath);
+    if (!parser) return null;
+    const profiler = new import_profiler.ColumnProfiler();
+    const allRows = [];
+    const maxRows = this.config.dataMaxRows ?? 1e6;
+    const { columns, totalRows } = await parser.parse(absPath, {
+      maxRows,
+      onBatch: (rows, cols) => {
+        profiler.addBatch(rows, cols);
+        allRows.push(...rows);
+      }
+    });
+    if (columns.length === 0) return null;
+    const columnProfiles = profiler.finalize(datasetId);
+    this.db.run("BEGIN");
+    try {
+      const rowTableName = `data_rows_${datasetId.replace(/[^a-zA-Z0-9_]/g, "_")}`;
+      this.db.run(`DROP TABLE IF EXISTS "${rowTableName}"`);
+      this.db.run("DELETE FROM data_columns WHERE dataset_id = ?", [datasetId]);
+      this.db.run("DELETE FROM data_datasets WHERE id = ?", [datasetId]);
+      this.db.run(`
+        INSERT INTO data_datasets (id, file_path, format, row_count, column_count, file_size, content_hash, summary, indexed_at)
+        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+      `, [datasetId, relPath, parser.name, totalRows, columns.length, stat.size, contentHash, null, Date.now()]);
+      for (const col of columnProfiles) {
+        this.db.run(`
+          INSERT INTO data_columns (id, dataset_id, name, position, inferred_type, nullable, null_count, null_pct, cardinality, min_value, max_value, mean_value, sample_values, summary, updated_at)
+          VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+        `, [
+          col.id,
+          col.datasetId,
+          col.name,
+          col.position,
+          col.inferredType,
+          col.nullable ? 1 : 0,
+          col.nullCount,
+          col.nullPct,
+          col.cardinality,
+          col.minValue,
+          col.maxValue,
+          col.meanValue,
+          JSON.stringify(col.sampleValues),
+          col.summary,
+          col.updatedAt
+        ]);
+      }
+      const colDefs = columns.map((c) => `"${c.replace(/"/g, '""')}" TEXT`).join(", ");
+      this.db.run(`CREATE TABLE "${rowTableName}" (rowid INTEGER PRIMARY KEY AUTOINCREMENT, ${colDefs})`);
+      const colNames = columns.map((c) => `"${c.replace(/"/g, '""')}"`).join(", ");
+      const placeholders = columns.map(() => "?").join(", ");
+      const insertStmt = `INSERT INTO "${rowTableName}" (${colNames}) VALUES (${placeholders})`;
+      for (const row of allRows) {
+        const values = columns.map((c) => {
+          const v = row[c];
+          if (v === null || v === void 0) return null;
+          if (typeof v === "object") return JSON.stringify(v);
+          return v;
+        });
+        this.db.run(insertStmt, values);
+      }
+      const historyColumns = columnProfiles.map((col) => ({
+        name: col.name,
+        type: col.inferredType,
+        cardinality: col.cardinality,
+        nullPct: col.nullPct
+      }));
+      this.db.run(`
+        INSERT INTO data_dataset_history (dataset_id, snapshot_at, row_count, column_count, columns_json, content_hash)
+        VALUES (?, ?, ?, ?, ?, ?)
+      `, [datasetId, Date.now(), totalRows, columns.length, JSON.stringify(historyColumns), contentHash]);
+      this.db.run("COMMIT");
+    } catch (err) {
+      this.db.run("ROLLBACK");
+      throw err;
+    }
+    return { rows: totalRows, columns: columns.length };
+  }
+  // ── Private ─────────────────────────────────────────────────────────────────
+  scanDataFiles() {
+    const includePatterns = this.config.dataInclude ?? [];
+    const excludePatterns = this.config.dataExclude ?? [];
+    const includeMatchers = includePatterns.map((p) => (0, import_picomatch.default)(p));
+    const excludeMatchers = excludePatterns.map((p) => (0, import_picomatch.default)(p));
+    const results = [];
+    const walk = (dir) => {
+      let entries;
+      try {
+        entries = fs.readdirSync(dir, { withFileTypes: true });
+      } catch {
+        return;
+      }
+      for (const entry of entries) {
+        const full = path.join(dir, entry.name);
+        const rel = path.relative(this.projectRoot, full).replace(/\\/g, "/");
+        if (entry.isDirectory()) {
+          if (excludeMatchers.some((m) => m(rel + "/"))) continue;
+          walk(full);
+        } else if (entry.isFile()) {
+          if (excludeMatchers.some((m) => m(rel))) continue;
+          if (includeMatchers.some((m) => m(rel))) {
+            if ((0, import_parsers.getDataParser)(rel)) {
+              results.push(rel);
+            }
+          }
+        }
+      }
+    };
+    walk(this.projectRoot);
+    return results;
+  }
+  removeDeletedDatasets(currentFiles) {
+    const currentSet = new Set(currentFiles.map((f) => generateDatasetId(f)));
+    const indexed = this.db.all("SELECT id FROM data_datasets").map((r) => r.id);
+    for (const id of indexed) {
+      if (!currentSet.has(id)) {
+        const rowTableName = `data_rows_${id.replace(/[^a-zA-Z0-9_]/g, "_")}`;
+        this.db.run(`DROP TABLE IF EXISTS "${rowTableName}"`);
+        this.db.run("DELETE FROM data_columns WHERE dataset_id = ?", [id]);
+        this.db.run("DELETE FROM data_code_refs WHERE dataset_id = ?", [id]);
+        this.db.run("DELETE FROM data_datasets WHERE id = ?", [id]);
+      }
+    }
+  }
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  DataIndexer
+});
+//# sourceMappingURL=indexer.js.map

package/dist/data/indexer.js.map

@@ -0,0 +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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+}