kirograph 0.12.1

package/dist/core/pipeline.js

@@ -0,0 +1,375 @@
+"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 pipeline_exports = {};
+__export(pipeline_exports, {
+  IndexPipeline: () => IndexPipeline
+});
+module.exports = __toCommonJS(pipeline_exports);
+var path = __toESM(require("path"));
+var fs = __toESM(require("fs"));
+var import_sync = require("../sync/index");
+var import_extractor = require("../extraction/extractor");
+var import_grammars = require("../extraction/grammars");
+var import_frameworks = require("../frameworks/index");
+var import_utils = require("../utils");
+const FILE_IO_BATCH_SIZE = 10;
+class IndexPipeline {
+  constructor(db, vectors, resolver, arch, lock, config, projectRoot) {
+    this.db = db;
+    this.vectors = vectors;
+    this.resolver = resolver;
+    this.arch = arch;
+    this.lock = lock;
+    this.config = config;
+    this.projectRoot = projectRoot;
+    this.mutex = new import_utils.Mutex();
+  }
+  async indexAll(opts) {
+    const release = await this.mutex.acquire();
+    this.lock.acquire();
+    const start = Date.now();
+    const errors = [];
+    let filesIndexed = 0;
+    let nodesCreated = 0;
+    let edgesCreated = 0;
+    const poisonedLanguages = /* @__PURE__ */ new Set();
+    try {
+      const files = await (0, import_sync.scanDirectory)(this.projectRoot, this.config, opts?.signal);
+      opts?.onProgress?.({ phase: "scanning", current: files.length, total: files.length });
+      const contentMap = /* @__PURE__ */ new Map();
+      for (let b = 0; b < files.length; b += FILE_IO_BATCH_SIZE) {
+        const batch = files.slice(b, b + FILE_IO_BATCH_SIZE);
+        const results = await Promise.all(batch.map((f) => fs.promises.readFile(f).catch(() => null)));
+        for (let i = 0; i < batch.length; i++) {
+          if (results[i]) contentMap.set(batch[i], results[i]);
+        }
+      }
+      for (let i = 0; i < files.length; i++) {
+        const file = files[i];
+        opts?.onProgress?.({ phase: "parsing", current: i + 1, total: files.length, currentFile: file });
+        try {
+          const content = contentMap.get(file);
+          if (!content) continue;
+          if (content.length > this.config.maxFileSize) continue;
+          const relPath = path.relative(this.projectRoot, file).replace(/\\/g, "/");
+          if (!opts?.force) {
+            const existing = this.db.getFile(relPath);
+            if (existing && (0, import_sync.hashContent)(content) === existing.contentHash) continue;
+          }
+          const { detectLanguage } = await Promise.resolve().then(() => require("../extraction/languages.js"));
+          const lang = detectLanguage(file);
+          if (poisonedLanguages.has(lang)) continue;
+          const extracted = await (0, import_extractor.extractFile)(file, this.projectRoot, content);
+          if (!extracted) continue;
+          const oldNodes = this.db.getNodesByFile(extracted.filePath);
+          if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map((n) => n.id));
+          this.db.transaction(() => {
+            this.db.deleteNodesByFile(extracted.filePath);
+            this.db.deleteUnresolvedRefsByFile(extracted.filePath);
+            this.db.upsertFile({
+              path: extracted.filePath,
+              contentHash: extracted.contentHash,
+              language: extracted.language,
+              fileSize: extracted.fileSize,
+              symbolCount: extracted.nodes.length,
+              indexedAt: Date.now()
+            });
+            for (const node of extracted.nodes) {
+              this.db.upsertNode(node);
+              nodesCreated++;
+            }
+            for (const edge of extracted.edges) {
+              this.db.insertEdge(edge);
+              edgesCreated++;
+            }
+            for (const ref of extracted.unresolvedRefs) {
+              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);
+            }
+          });
+          filesIndexed++;
+        } catch (err) {
+          const msg = err instanceof Error ? err.message : String(err);
+          errors.push(`${file}: ${msg}`);
+          const isWasmCrash = err?.constructor?.name === "RuntimeError" || msg.includes("Aborted(") || msg.includes("RuntimeError") || msg.includes("WASM grammar exists but failed to load");
+          if (isWasmCrash) {
+            const { detectLanguage } = await Promise.resolve().then(() => require("../extraction/languages.js"));
+            const lang = detectLanguage(file);
+            poisonedLanguages.add(lang);
+            (0, import_grammars.clearParserCache)();
+            try {
+              await (0, import_grammars.initGrammars)();
+              poisonedLanguages.clear();
+            } catch {
+              errors.push("WASM runtime unrecoverable after crash \u2014 aborting batch");
+              break;
+            }
+          }
+        }
+      }
+      const emptyFiles = this.db.getAllFiles().filter(
+        (f) => f.symbolCount === 0 && (0, import_grammars.hasWasmGrammar)(f.language)
+      );
+      if (emptyFiles.length > 0) {
+        opts?.onProgress?.({ phase: "retrying", current: 0, total: emptyFiles.length });
+        for (let i = 0; i < emptyFiles.length; i++) {
+          const ef = emptyFiles[i];
+          const absPath = path.join(this.projectRoot, ef.path);
+          opts?.onProgress?.({ phase: "retrying", current: i + 1, total: emptyFiles.length, currentFile: absPath });
+          try {
+            const extracted = await (0, import_extractor.extractFile)(absPath, this.projectRoot);
+            if (!extracted || extracted.nodes.length === 0) continue;
+            const oldNodes = this.db.getNodesByFile(extracted.filePath);
+            if (oldNodes.length > 0) await this.vectors.deleteEmbeddings(oldNodes.map((n) => n.id));
+            this.db.transaction(() => {
+              this.db.deleteNodesByFile(extracted.filePath);
+              this.db.deleteUnresolvedRefsByFile(extracted.filePath);
+              this.db.upsertFile({
+                path: extracted.filePath,
+                contentHash: extracted.contentHash,
+                language: extracted.language,
+                fileSize: extracted.fileSize,
+                symbolCount: extracted.nodes.length,
+                indexedAt: Date.now()
+              });
+              for (const node of extracted.nodes) {
+                this.db.upsertNode(node);
+                nodesCreated++;
+              }
+              for (const edge of extracted.edges) {
+                this.db.insertEdge(edge);
+                edgesCreated++;
+              }
+              for (const ref of extracted.unresolvedRefs) {
+                this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);
+              }
+            });
+            filesIndexed++;
+          } catch {
+          }
+        }
+      }
+      opts?.onProgress?.({ phase: "resolving", current: 0, total: 1 });
+      await this.resolver.resolveAll((current, total) => {
+        opts?.onProgress?.({ phase: "resolving", current, total });
+      });
+      opts?.onProgress?.({ phase: "detecting frameworks", current: 0, total: 1 });
+      const detectedFrameworks = await (0, import_frameworks.detectFrameworks)(this.projectRoot, this.db);
+      const languages = [...new Set(this.db.getAllFiles().map((f) => f.language).filter(Boolean))];
+      opts?.onProgress?.({
+        phase: "detecting frameworks",
+        current: 1,
+        total: 1,
+        meta: { frameworks: detectedFrameworks.map((f) => f.name), languages }
+      });
+      if (this.vectors.isInitialized()) {
+        opts?.onProgress?.({ phase: "embeddings", current: 0, total: 1 });
+        await this.vectors.embedAll(
+          (current, total) => opts?.onProgress?.({ phase: "embeddings", current, total })
+        );
+      }
+      if (this.config.enableArchitecture) {
+        opts?.onProgress?.({ phase: "architecture", current: 0, total: 1 });
+        await this.arch.analyze(
+          (msg) => opts?.onProgress?.({ phase: "architecture", current: 0, total: 1, meta: { msg } })
+        );
+        opts?.onProgress?.({ phase: "architecture", current: 1, total: 1 });
+      }
+      this.lock.clearDirty();
+      return { success: errors.length === 0, filesIndexed, nodesCreated, edgesCreated, errors, duration: Date.now() - start };
+    } finally {
+      this.lock.release();
+      release();
+    }
+  }
+  async sync(opts) {
+    const release = await this.mutex.acquire();
+    this.lock.acquire();
+    const start = Date.now();
+    const changedFiles = opts?.changedFiles;
+    const onProgress = opts?.onProgress;
+    const result = {
+      added: [],
+      modified: [],
+      removed: [],
+      nodesCreated: 0,
+      nodesUpdated: 0,
+      nodesRemoved: 0,
+      edgesCreated: 0,
+      edgesRemoved: 0,
+      filesScanned: 0,
+      errors: [],
+      duration: 0
+    };
+    try {
+      const removeFile = async (rel) => {
+        const oldNodes = this.db.getNodesByFile(rel);
+        const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map((n) => n.id)).length;
+        result.nodesRemoved += oldNodes.length;
+        result.edgesRemoved += oldEdgeCount;
+        await this.vectors.deleteEmbeddings(oldNodes.map((n) => n.id));
+        this.db.deleteFile(rel);
+        this.db.deleteUnresolvedRefsByFile(rel);
+        result.removed.push(rel);
+      };
+      const allIndexed = this.db.getAllFiles();
+      for (const f of allIndexed) {
+        if (!(0, import_sync.shouldIncludeFile)(f.path, this.config)) {
+          onProgress?.({ phase: "scanning", current: 0, total: 0, meta: { excludeCleanup: true, file: f.path } });
+          await removeFile(f.path);
+        }
+      }
+      let filesToProcess;
+      onProgress?.({ phase: "scanning", current: 0, total: 0 });
+      if (changedFiles) {
+        filesToProcess = changedFiles.map((f) => path.resolve(this.projectRoot, f));
+      } else {
+        const gitChanged = await (0, import_sync.getChangedFiles)(this.projectRoot, this.config);
+        const hasChanges = gitChanged.added.length > 0 || gitChanged.modified.length > 0 || gitChanged.removed.length > 0;
+        if (hasChanges) {
+          for (const p of gitChanged.removed) {
+            await removeFile(path.relative(this.projectRoot, p).replace(/\\/g, "/"));
+          }
+          filesToProcess = [...gitChanged.added, ...gitChanged.modified];
+        } else {
+          const indexed = new Set(this.db.getAllFiles().map((f) => f.path));
+          const current = new Set(
+            (await (0, import_sync.scanDirectory)(this.projectRoot, this.config)).map((f) => path.relative(this.projectRoot, f).replace(/\\/g, "/"))
+          );
+          result.filesScanned = current.size;
+          for (const p of indexed) {
+            if (!current.has(p)) await removeFile(p);
+          }
+          filesToProcess = await (0, import_sync.scanDirectory)(this.projectRoot, this.config);
+        }
+      }
+      result.filesScanned = result.filesScanned || filesToProcess.length;
+      onProgress?.({ phase: "scanning", current: result.filesScanned, total: result.filesScanned });
+      const poisonedLanguages = /* @__PURE__ */ new Set();
+      for (let i = 0; i < filesToProcess.length; i++) {
+        const file = filesToProcess[i];
+        onProgress?.({ phase: "parsing", current: i + 1, total: filesToProcess.length, currentFile: file });
+        if (!fs.existsSync(file)) {
+          const rel = path.relative(this.projectRoot, file).replace(/\\/g, "/");
+          await removeFile(rel);
+          continue;
+        }
+        try {
+          const { detectLanguage } = await Promise.resolve().then(() => require("../extraction/languages.js"));
+          const lang = detectLanguage(file);
+          if (poisonedLanguages.has(lang)) continue;
+          const extracted = await (0, import_extractor.extractFile)(file, this.projectRoot);
+          if (!extracted) continue;
+          const existing = this.db.getFile(extracted.filePath);
+          const isNew = !existing;
+          if (!isNew && existing.contentHash === extracted.contentHash) continue;
+          const oldNodes = this.db.getNodesByFile(extracted.filePath);
+          const oldEdgeCount = this.db.getEdgesForNodes(oldNodes.map((n) => n.id)).length;
+          await this.vectors.deleteEmbeddings(oldNodes.map((n) => n.id));
+          this.db.transaction(() => {
+            result.nodesRemoved += oldNodes.length;
+            result.edgesRemoved += oldEdgeCount;
+            this.db.deleteNodesByFile(extracted.filePath);
+            this.db.deleteUnresolvedRefsByFile(extracted.filePath);
+            this.db.upsertFile({
+              path: extracted.filePath,
+              contentHash: extracted.contentHash,
+              language: extracted.language,
+              fileSize: extracted.fileSize,
+              symbolCount: extracted.nodes.length,
+              indexedAt: Date.now()
+            });
+            for (const node of extracted.nodes) {
+              this.db.upsertNode(node);
+              result.nodesCreated++;
+            }
+            for (const edge of extracted.edges) {
+              this.db.insertEdge(edge);
+              result.edgesCreated++;
+            }
+            for (const ref of extracted.unresolvedRefs) {
+              this.db.insertUnresolvedRef(ref.sourceId, ref.refName, ref.refKind, extracted.filePath, ref.line, ref.column);
+            }
+          });
+          this.resolver.invalidateFile(extracted.filePath);
+          if (isNew) result.added.push(extracted.filePath);
+          else {
+            result.modified.push(extracted.filePath);
+            result.nodesUpdated += extracted.nodes.length;
+          }
+        } catch (err) {
+          const msg = err instanceof Error ? err.message : String(err);
+          result.errors.push(`${file}: ${msg}`);
+          const isWasmCrash = err?.constructor?.name === "RuntimeError" || msg.includes("Aborted(") || msg.includes("RuntimeError") || msg.includes("WASM grammar exists but failed to load");
+          if (isWasmCrash) {
+            const { detectLanguage } = await Promise.resolve().then(() => require("../extraction/languages.js"));
+            const lang = detectLanguage(file);
+            poisonedLanguages.add(lang);
+            (0, import_grammars.clearParserCache)();
+            try {
+              await (0, import_grammars.initGrammars)();
+              poisonedLanguages.clear();
+            } catch {
+              result.errors.push("WASM runtime unrecoverable after crash \u2014 aborting sync");
+              break;
+            }
+          }
+        }
+      }
+      onProgress?.({ phase: "resolving", current: 0, total: 1 });
+      await this.resolver.resolveAll((current, total) => {
+        onProgress?.({ phase: "resolving", current, total });
+      });
+      await (0, import_frameworks.detectFrameworks)(this.projectRoot);
+      if (this.vectors.isInitialized()) {
+        onProgress?.({ phase: "embeddings", current: 0, total: 1 });
+        await this.vectors.embedAll(
+          (current, total) => onProgress?.({ phase: "embeddings", current, total })
+        );
+      }
+      if (this.config.enableArchitecture) {
+        onProgress?.({ phase: "architecture", current: 0, total: 1 });
+        await this.arch.analyze(
+          (msg) => onProgress?.({ phase: "architecture", current: 0, total: 1, meta: { msg } })
+        );
+        onProgress?.({ phase: "architecture", current: 1, total: 1 });
+      }
+      this.lock.clearDirty();
+      result.duration = Date.now() - start;
+      return result;
+    } finally {
+      this.lock.release();
+      release();
+    }
+  }
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  IndexPipeline
+});
+//# sourceMappingURL=pipeline.js.map

package/dist/core/pipeline.js.map

@@ -0,0 +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      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      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/core/snapshot.js

@@ -0,0 +1,141 @@
+"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 snapshot_exports = {};
+__export(snapshot_exports, {
+  SnapshotManager: () => SnapshotManager
+});
+module.exports = __toCommonJS(snapshot_exports);
+var fs = __toESM(require("fs"));
+var path = __toESM(require("path"));
+const SNAPSHOTS_DIR = "snapshots";
+class SnapshotManager {
+  constructor(db, projectRoot) {
+    this.db = db;
+    this.snapshotsDir = path.join(projectRoot, ".kirograph", SNAPSHOTS_DIR);
+  }
+  ensureDir() {
+    fs.mkdirSync(this.snapshotsDir, { recursive: true });
+  }
+  save(label) {
+    this.ensureDir();
+    const timestamp = Date.now();
+    const snapshotLabel = label ?? new Date(timestamp).toISOString().slice(0, 19).replace(/[T:]/g, "-");
+    const nodes = this.db.getAllNodes().map((n) => ({
+      id: n.id,
+      name: n.name,
+      kind: n.kind,
+      filePath: n.filePath
+    }));
+    const edges = this.db.getAllEdges().map((e) => ({
+      source: e.source,
+      target: e.target,
+      kind: e.kind
+    }));
+    const snapshot = {
+      label: snapshotLabel,
+      timestamp,
+      nodeCount: nodes.length,
+      edgeCount: edges.length,
+      nodes,
+      edges
+    };
+    const filename = `${snapshotLabel}.json`;
+    fs.writeFileSync(path.join(this.snapshotsDir, filename), JSON.stringify(snapshot));
+    return snapshot;
+  }
+  list() {
+    if (!fs.existsSync(this.snapshotsDir)) return [];
+    return fs.readdirSync(this.snapshotsDir).filter((f) => f.endsWith(".json")).flatMap((f) => {
+      try {
+        const data = JSON.parse(fs.readFileSync(path.join(this.snapshotsDir, f), "utf8"));
+        return [{ label: data.label, timestamp: data.timestamp, nodeCount: data.nodeCount, edgeCount: data.edgeCount }];
+      } catch {
+        return [];
+      }
+    }).sort((a, b) => b.timestamp - a.timestamp);
+  }
+  load(label) {
+    const candidates = [
+      path.join(this.snapshotsDir, `${label}.json`),
+      path.join(this.snapshotsDir, label)
+    ];
+    for (const p of candidates) {
+      if (fs.existsSync(p)) {
+        try {
+          return JSON.parse(fs.readFileSync(p, "utf8"));
+        } catch {
+          return null;
+        }
+      }
+    }
+    return null;
+  }
+  loadLatest() {
+    const all = this.list();
+    return all.length > 0 ? this.load(all[0].label) : null;
+  }
+  currentSnapshot() {
+    const nodes = this.db.getAllNodes().map((n) => ({
+      id: n.id,
+      name: n.name,
+      kind: n.kind,
+      filePath: n.filePath
+    }));
+    const edges = this.db.getAllEdges().map((e) => ({
+      source: e.source,
+      target: e.target,
+      kind: e.kind
+    }));
+    return { label: "current", timestamp: Date.now(), nodeCount: nodes.length, edgeCount: edges.length, nodes, edges };
+  }
+  diff(from, to) {
+    const fromNodeIds = new Set(from.nodes.map((n) => n.id));
+    const toNodeIds = new Set(to.nodes.map((n) => n.id));
+    const addedNodes = to.nodes.filter((n) => !fromNodeIds.has(n.id));
+    const removedNodes = from.nodes.filter((n) => !toNodeIds.has(n.id));
+    const edgeKey = (e) => `${e.source}|${e.target}|${e.kind}`;
+    const fromEdgeKeys = new Set(from.edges.map(edgeKey));
+    const toEdgeKeys = new Set(to.edges.map(edgeKey));
+    const addedEdges = to.edges.filter((e) => !fromEdgeKeys.has(edgeKey(e)));
+    const removedEdges = from.edges.filter((e) => !toEdgeKeys.has(edgeKey(e)));
+    return {
+      from: { label: from.label, timestamp: from.timestamp },
+      to: { label: to.label, timestamp: to.timestamp },
+      addedNodes,
+      removedNodes,
+      addedEdges,
+      removedEdges
+    };
+  }
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  SnapshotManager
+});
+//# sourceMappingURL=snapshot.js.map

package/dist/core/snapshot.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/core/snapshot.ts"],
+  "sourcesContent": ["/**\n * KiroGraph Snapshot Manager\n *\n * Saves lightweight graph snapshots (node IDs + edge tuples) to\n * .kirograph/snapshots/ and computes structural diffs between them.\n */\n\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport type { GraphDatabase } from '../db/database';\n\nexport interface SnapshotNode {\n  id: string;\n  name: string;\n  kind: string;\n  filePath: string;\n}\n\nexport interface SnapshotEdge {\n  source: string;\n  target: string;\n  kind: string;\n}\n\nexport interface GraphSnapshot {\n  label: string;\n  timestamp: number;\n  nodeCount: number;\n  edgeCount: number;\n  nodes: SnapshotNode[];\n  edges: SnapshotEdge[];\n}\n\nexport interface GraphDiff {\n  from: { label: string; timestamp: number };\n  to: { label: string; timestamp: number };\n  addedNodes: SnapshotNode[];\n  removedNodes: SnapshotNode[];\n  addedEdges: SnapshotEdge[];\n  removedEdges: SnapshotEdge[];\n}\n\nconst SNAPSHOTS_DIR = 'snapshots';\n\nexport class SnapshotManager {\n  private readonly snapshotsDir: string;\n\n  constructor(private readonly db: GraphDatabase, projectRoot: string) {\n    this.snapshotsDir = path.join(projectRoot, '.kirograph', SNAPSHOTS_DIR);\n  }\n\n  private ensureDir(): void {\n    fs.mkdirSync(this.snapshotsDir, { recursive: true });\n  }\n\n  save(label?: string): GraphSnapshot {\n    this.ensureDir();\n    const timestamp = Date.now();\n    const snapshotLabel = label ?? new Date(timestamp).toISOString().slice(0, 19).replace(/[T:]/g, '-');\n\n    const nodes: SnapshotNode[] = this.db.getAllNodes().map(n => ({\n      id: n.id,\n      name: n.name,\n      kind: n.kind,\n      filePath: n.filePath,\n    }));\n    const edges: SnapshotEdge[] = this.db.getAllEdges().map(e => ({\n      source: e.source,\n      target: e.target,\n      kind: e.kind,\n    }));\n\n    const snapshot: GraphSnapshot = {\n      label: snapshotLabel,\n      timestamp,\n      nodeCount: nodes.length,\n      edgeCount: edges.length,\n      nodes,\n      edges,\n    };\n\n    const filename = `${snapshotLabel}.json`;\n    fs.writeFileSync(path.join(this.snapshotsDir, filename), JSON.stringify(snapshot));\n    return snapshot;\n  }\n\n  list(): Array<{ label: string; timestamp: number; nodeCount: number; edgeCount: number }> {\n    if (!fs.existsSync(this.snapshotsDir)) return [];\n    return fs.readdirSync(this.snapshotsDir)\n      .filter(f => f.endsWith('.json'))\n      .flatMap(f => {\n        try {\n          const data: GraphSnapshot = JSON.parse(fs.readFileSync(path.join(this.snapshotsDir, f), 'utf8'));\n          return [{ label: data.label, timestamp: data.timestamp, nodeCount: data.nodeCount, edgeCount: data.edgeCount }];\n        } catch { return []; }\n      })\n      .sort((a, b) => b.timestamp - a.timestamp);\n  }\n\n  load(label: string): GraphSnapshot | null {\n    const candidates = [\n      path.join(this.snapshotsDir, `${label}.json`),\n      path.join(this.snapshotsDir, label),\n    ];\n    for (const p of candidates) {\n      if (fs.existsSync(p)) {\n        try { return JSON.parse(fs.readFileSync(p, 'utf8')); } catch { return null; }\n      }\n    }\n    return null;\n  }\n\n  loadLatest(): GraphSnapshot | null {\n    const all = this.list();\n    return all.length > 0 ? this.load(all[0].label) : null;\n  }\n\n  currentSnapshot(): GraphSnapshot {\n    const nodes: SnapshotNode[] = this.db.getAllNodes().map(n => ({\n      id: n.id, name: n.name, kind: n.kind, filePath: n.filePath,\n    }));\n    const edges: SnapshotEdge[] = this.db.getAllEdges().map(e => ({\n      source: e.source, target: e.target, kind: e.kind,\n    }));\n    return { label: 'current', timestamp: Date.now(), nodeCount: nodes.length, edgeCount: edges.length, nodes, edges };\n  }\n\n  diff(from: GraphSnapshot, to: GraphSnapshot): GraphDiff {\n    const fromNodeIds = new Set(from.nodes.map(n => n.id));\n    const toNodeIds = new Set(to.nodes.map(n => n.id));\n\n    const addedNodes = to.nodes.filter(n => !fromNodeIds.has(n.id));\n    const removedNodes = from.nodes.filter(n => !toNodeIds.has(n.id));\n\n    const edgeKey = (e: SnapshotEdge) => `${e.source}|${e.target}|${e.kind}`;\n    const fromEdgeKeys = new Set(from.edges.map(edgeKey));\n    const toEdgeKeys = new Set(to.edges.map(edgeKey));\n\n    const addedEdges = to.edges.filter(e => !fromEdgeKeys.has(edgeKey(e)));\n    const removedEdges = from.edges.filter(e => !toEdgeKeys.has(edgeKey(e)));\n\n    return {\n      from: { label: from.label, timestamp: from.timestamp },\n      to: { label: to.label, timestamp: to.timestamp },\n      addedNodes,\n      removedNodes,\n      addedEdges,\n      removedEdges,\n    };\n  }\n}\n"],
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+}