@goshenkata/dryscan-core 1.2.4 → 1.2.5

package/dist/index.js

@@ -368,6 +368,7 @@ var JavaExtractor = class {
       filePath: file,
       startLine,
       endLine,
+      children: [],
       code: this.stripComments(source.slice(node.startIndex, node.endIndex)),
       unitType: "function" /* FUNCTION */,
       parentId: parentClass?.id,
@@ -402,9 +403,11 @@ var JavaExtractor = class {
             parentId: parentFunction.id,
             parent: parentFunction
           };
+          const contextLength = this.config?.contextLength ?? 2048;
+          const splitBlocks = this.textSplitBlockIfOverContextLimit(blockUnit, contextLength);
           parentFunction.children = parentFunction.children || [];
-          parentFunction.children.push(blockUnit);
-          blocks.push(blockUnit);
+          parentFunction.children.push(...splitBlocks);
+          blocks.push(...splitBlocks);
         }
       }
       for (let i = 0; i < n.namedChildCount; i++) {
@@ -450,6 +453,21 @@ var JavaExtractor = class {
   removeDuplicates(units) {
     return Array.from(new Map(units.map((u) => [u.id, u])).values());
   }
+  /** Splits a block unit's code into chunks if it exceeds the context length limit. */
+  textSplitBlockIfOverContextLimit(unit, contextLength) {
+    if (unit.code.length <= contextLength) return [unit];
+    const chunks = [];
+    let chunkIndex = 0;
+    for (let i = 0; i < unit.code.length; i += contextLength) {
+      chunks.push({
+        ...unit,
+        id: `${unit.id}:chunk${chunkIndex}`,
+        code: unit.code.slice(i, i + contextLength)
+      });
+      chunkIndex++;
+    }
+    return chunks;
+  }
 };
 
 // src/Gitignore.ts
@@ -1237,19 +1255,25 @@ var DuplicateService = class {
   }
   config;
   cache = DuplicationCache.getInstance();
+  //todo vetter optimisation
   async findDuplicates(config) {
     this.config = config;
+    const t0 = performance.now();
     const allUnits = await this.deps.db.getAllUnits();
+    log5("Starting duplicate analysis on %d units", allUnits.length);
     if (allUnits.length < 2) {
+      log5("Not enough units to compare, returning empty result");
       const score2 = this.computeDuplicationScore([], allUnits);
       return { duplicates: [], score: score2 };
     }
     const thresholds = this.resolveThresholds(config.threshold);
+    log5("Resolved thresholds: function=%d, block=%d, class=%d", thresholds.function, thresholds.block, thresholds.class);
     const duplicates = this.computeDuplicates(allUnits, thresholds);
     const filteredDuplicates = duplicates.filter((group) => !this.isGroupExcluded(group));
-    log5("Found %d duplicate groups", filteredDuplicates.length);
+    log5("Found %d duplicate groups (%d excluded)", filteredDuplicates.length, duplicates.length - filteredDuplicates.length);
     this.cache.update(filteredDuplicates).catch((err) => log5("Cache update failed: %O", err));
     const score = this.computeDuplicationScore(filteredDuplicates, allUnits);
+    log5("findDuplicates completed in %dms", (performance.now() - t0).toFixed(2));
     return { duplicates: filteredDuplicates, score };
   }
   resolveThresholds(functionThreshold) {
@@ -1273,25 +1297,37 @@ var DuplicateService = class {
       list.push(unit);
       byType.set(unit.unitType, list);
     }
+    const t0 = performance.now();
     for (const [type, typedUnits] of byType.entries()) {
       const threshold = this.getThreshold(type, thresholds);
+      log5("Comparing %d units of type '%s' with threshold %d", typedUnits.length, type, threshold);
+      const typeStart = performance.now();
       for (let i = 0; i < typedUnits.length; i++) {
         for (let j = i + 1; j < typedUnits.length; j++) {
           const left = typedUnits[i];
           const right = typedUnits[j];
-          if (this.shouldSkipComparison(left, right)) continue;
+          if (this.shouldSkipComparison(left, right)) {
+            log5("Skipping nested block comparison: '%s' and '%s'", left.name, right.name);
+            continue;
+          }
           const cached = this.cache.get(left.id, right.id, left.filePath, right.filePath);
           let similarity = null;
           if (cached !== null) {
+            log5("Cache hit for '%s' <-> '%s': similarity=%d", left.name, right.name, cached);
             similarity = cached;
           } else {
-            if (!left.embedding || !right.embedding) continue;
+            if (!left.embedding || !right.embedding) {
+              log5("Skipping '%s' <-> '%s': missing embedding", left.name, right.name);
+              continue;
+            }
             similarity = this.computeWeightedSimilarity(left, right);
+            log5("Computed similarity for '%s' <-> '%s': %d", left.name, right.name, similarity);
           }
           if (similarity === null) continue;
           if (similarity >= threshold) {
             const exclusionString = this.deps.pairing.pairKeyForUnits(left, right);
             if (!exclusionString) continue;
+            log5("Duplicate found: '%s' <-> '%s' (similarity=%d)", left.name, right.name, similarity);
             duplicates.push({
               id: `${left.id}::${right.id}`,
               similarity,
@@ -1319,7 +1355,9 @@ var DuplicateService = class {
           }
         }
       }
+      log5("Type '%s' comparisons completed in %dms", type, (performance.now() - typeStart).toFixed(2));
     }
+    log5("computeDuplicates completed in %dms, found %d raw duplicates", (performance.now() - t0).toFixed(2), duplicates.length);
     return duplicates.sort((a, b) => b.similarity - a.similarity);
   }
   isGroupExcluded(group) {

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/DryScan.ts","../src/const.ts","../src/IndexUnitExtractor.ts","../src/extractors/java.ts","../src/config/indexConfig.ts","../src/config/configStore.ts","../src/config/dryconfig.ts","../src/Gitignore.ts","../src/db/DryScanDatabase.ts","../src/db/entities/FileEntity.ts","../src/db/entities/IndexUnitEntity.ts","../src/services/RepositoryInitializer.ts","../src/services/EmbeddingService.ts","../src/services/UpdateService.ts","../src/DryScanUpdater.ts","../src/services/DuplicationCache.ts","../src/services/DuplicateService.ts","../src/services/ExclusionService.ts","../src/services/PairingService.ts"],"sourcesContent":["import upath from \"upath\";\nimport fs from \"fs/promises\";\nimport { DuplicateAnalysisResult, DuplicateReport } from \"./types\";\nimport { DRYSCAN_DIR, INDEX_DB } from \"./const\";\nimport { defaultExtractors, IndexUnitExtractor } from \"./IndexUnitExtractor\";\nimport { DryScanDatabase } from \"./db/DryScanDatabase\";\nimport { RepositoryInitializer, InitOptions as InitServiceOptions } from \"./services/RepositoryInitializer\";\nimport { UpdateService } from \"./services/UpdateService\";\nimport { DuplicateService } from \"./services/DuplicateService\";\nimport { ExclusionService } from \"./services/ExclusionService\";\nimport { DryScanServiceDeps } from \"./services/types\";\nimport { configStore } from \"./config/configStore\";\nimport { DryConfig } from \"./types\";\nimport { PairingService } from \"./services/PairingService\";\nimport { existsSync } from \"fs\";\n\nexport type InitOptions = InitServiceOptions;\n\n\nexport class DryScan {\n  repoPath: string;\n  private readonly extractor: IndexUnitExtractor;\n  private db: DryScanDatabase;\n  private readonly services: {\n    initializer: RepositoryInitializer;\n    updater: UpdateService;\n    duplicate: DuplicateService;\n    exclusion: ExclusionService;\n  };\n  private readonly serviceDeps: DryScanServiceDeps;\n\n  constructor(\n    repoPath: string,\n    extractor?: IndexUnitExtractor,\n    db?: DryScanDatabase\n  ) {\n    this.repoPath = repoPath;\n    this.extractor = extractor ?? new IndexUnitExtractor(repoPath, defaultExtractors(repoPath));\n    this.db = db ?? new DryScanDatabase();\n\n    this.serviceDeps = {\n      repoPath: this.repoPath,\n      db: this.db,\n      extractor: this.extractor,\n      pairing: new PairingService(this.extractor),\n    };\n\n    const exclusion = new ExclusionService(this.serviceDeps);\n    this.services = {\n      initializer: new RepositoryInitializer(this.serviceDeps, exclusion),\n      updater: new UpdateService(this.serviceDeps, exclusion),\n      duplicate: new DuplicateService(this.serviceDeps),\n      exclusion,\n    };\n  }\n\n  /**\n   * Initializes the DryScan repository with a 3-phase analysis:\n   * Phase 1: Extract and save all functions\n   * Phase 2: Resolve and save internal dependencies\n   * Phase 3: Compute and save semantic embeddings\n   */\n  async init(options?: InitOptions): Promise<void> {\n    console.log(`[DryScan] Initializing repository at ${this.repoPath}`);\n\n    const dryDir = upath.join(this.repoPath, DRYSCAN_DIR);\n    if (existsSync(dryDir)) {\n      console.warn(`[DryScan] Warning: a '.dry' folder already exists at ${dryDir}.`);\n    }\n    console.log(\"[DryScan] Preparing database and cache...\");\n    await configStore.init(this.repoPath);\n    await this.ensureDatabase();\n    console.log(\"[DryScan] Starting initial scan (may take a moment)...\");\n    await this.services.initializer.init(options);\n    console.log(\"[DryScan] Initial scan complete.\");\n  }\n\n  /**\n   * Updates the index by detecting changed, new, and deleted files.\n   * Only reprocesses units in changed files for efficiency.\n   * Delegates to DryScanUpdater module for implementation.\n   * \n   * Update process:\n   * 1. List all current source files in repository\n   * 2. For each file, check if it's new, changed, or unchanged (via mtime + checksum)\n   * 3. Remove old units from changed/deleted files\n   * 4. Extract and save units from new/changed files\n   * 5. Recompute internal dependencies for affected units\n   * 6. Recompute embeddings for affected units\n   * 7. Update file tracking metadata\n   */\n  async updateIndex(): Promise<void> {\n    console.log(`[DryScan] Updating index at ${this.repoPath}...`);\n    console.log(\"[DryScan] Checking for file changes...\");\n    const start = Date.now();\n    await this.ensureDatabase();\n    await this.services.updater.updateIndex();\n    const duration = Date.now() - start;\n    console.log(`[DryScan] Index update complete. Took ${duration}ms.`);\n  }\n\n\n  /**\n   * Runs duplicate detection and returns a normalized report payload ready for persistence or display.\n   */\n  async buildDuplicateReport(): Promise<DuplicateReport> {\n    const config = await this.loadConfig();\n    const analysis = await this.findDuplicates(config);\n    return {\n      version: 1,\n      generatedAt: new Date().toISOString(),\n      threshold: config.threshold,\n      grade: analysis.score.grade,\n      score: analysis.score,\n      duplicates: analysis.duplicates,\n    };\n  }\n\n  /**\n   * Finds duplicate code blocks using cosine similarity on embeddings.\n   * Automatically updates the index before searching to ensure results are current.\n   * Compares all function pairs and returns groups with similarity above the configured threshold.\n   *\n   * @returns Analysis result with duplicate groups and duplication score\n   */\n  private async findDuplicates(config: DryConfig): Promise<DuplicateAnalysisResult> {\n    console.log(`[DryScan] Finding duplicates (threshold: ${config.threshold})...`);\n    await this.ensureDatabase();\n\n    console.log(\"[DryScan] Updating index...\");\n    const updateStart = Date.now();\n    await this.updateIndex();\n    const updateDuration = Date.now() - updateStart;\n    console.log(`[DryScan] Index update  took ${updateDuration}ms.`);\n\n    console.log(\"[DryScan] Detecting duplicates...\");\n    const dupStart = Date.now();\n    const result = await this.services.duplicate.findDuplicates(config);\n    const dupDuration = Date.now() - dupStart;\n    console.log(`[DryScan] Duplicate detection took ${dupDuration}ms.`);\n\n    return result;\n  }\n\n  /**\n   * Cleans excludedPairs entries that no longer match any indexed units.\n   * Runs an update first to ensure the index reflects current code.\n   */\n  async cleanExclusions(): Promise<{ removed: number; kept: number }> {\n    await this.updateIndex();\n    return this.services.exclusion.cleanExclusions();\n  }\n\n  private async ensureDatabase(): Promise<void> {\n    if (this.db.isInitialized()) return;\n    const dbPath = upath.join(this.repoPath, DRYSCAN_DIR, INDEX_DB);\n    await fs.mkdir(upath.dirname(dbPath), { recursive: true });\n    await this.db.init(dbPath);\n  }\n\n  private async loadConfig(): Promise<DryConfig> {\n    return configStore.get(this.repoPath);\n  }\n\n}\n","export const DRYSCAN_DIR = \".dry\";\nexport const INDEX_DB = \"index.db\";\nexport const REPORTS_DIR = \"reports\";\nexport const FILE_CHECKSUM_ALGO = \"md5\";\nexport const BLOCK_HASH_ALGO = \"sha1\";","import path from \"path\";\nimport type { Stats } from \"fs\";\nimport fs from \"fs/promises\";\nimport upath from \"upath\";\nimport crypto from \"node:crypto\";\nimport debug from \"debug\";\nimport { glob } from \"glob-gitignore\";\nimport { IndexUnit } from \"./types\";\nimport { LanguageExtractor } from \"./extractors/LanguageExtractor\";\nimport { JavaExtractor } from \"./extractors/java\";\nimport { FILE_CHECKSUM_ALGO } from \"./const\";\nimport { configStore } from \"./config/configStore\";\nimport { DryConfig } from \"./types\";\nimport { Gitignore } from \"./Gitignore\"\nimport { Ignore } from \"ignore\";\n\nconst log = debug(\"DryScan:Extractor\");\n\nexport type { LanguageExtractor } from \"./extractors/LanguageExtractor\";\n/**\n * Returns the default set of language extractors supported by DryScan.\n * Extend/override by passing custom extractors into the IndexUnitExtractor constructor.\n */\nexport function defaultExtractors(repoPath: string): LanguageExtractor[] {\n  return [new JavaExtractor(repoPath)];\n}\n\n/**\n * Extracts and indexes code units (classes, functions, blocks) for a repository.\n * Owns shared file-system helpers and delegates language-specific parsing to LanguageExtractors.\n */\nexport class IndexUnitExtractor {\n  private readonly root: string;\n  readonly extractors: LanguageExtractor[];\n  private readonly gitignore: Gitignore;\n\n  constructor(\n    rootPath: string,\n    extractors?: LanguageExtractor[]\n  ) {\n    this.root = rootPath;\n    this.extractors = extractors ?? defaultExtractors(rootPath);\n    this.gitignore = new Gitignore(this.root);\n    log(\"Initialized extractor for %s\", this.root);\n  }\n\n  /**\n   * Lists all supported source files from a path. Honors exclusion globs from config.\n   */\n  async listSourceFiles(dirPath: string): Promise<string[]> {\n    const target = await this.resolveTarget(dirPath);\n    const config = await this.loadConfig();\n    const ignoreMatcher = await this.gitignore.buildMatcher(config);\n\n    if (target.stat.isFile()) {\n      return this.filterSingleFile(target.baseRel, ignoreMatcher);\n    }\n\n    const matches = await this.globSourceFiles(target.baseRel);\n    return this.filterSupportedFiles(matches, ignoreMatcher);\n  }\n\n  /**\n   * Computes MD5 checksum of file content to track changes.\n   */\n  async computeChecksum(filePath: string): Promise<string> {\n    const fullPath = path.isAbsolute(filePath)\n      ? filePath\n      : path.join(this.root, filePath);\n\n    const content = await fs.readFile(fullPath, \"utf8\");\n    return crypto.createHash(FILE_CHECKSUM_ALGO).update(content).digest(\"hex\");\n  }\n\n  /**\n   * Scans a file or directory and extracts indexable units using the matching LanguageExtractor.\n   * The returned units have repo-relative file paths and no embedding attached.\n   */\n  async scan(targetPath: string): Promise<IndexUnit[]> {\n    const fullPath = path.isAbsolute(targetPath)\n      ? targetPath\n      : path.join(this.root, targetPath);\n\n    const stat = await fs.stat(fullPath).catch(() => null);\n    if (!stat) {\n      throw new Error(`Path not found: ${fullPath}`);\n    }\n\n    if (stat.isDirectory()) {\n      log(\"Scanning directory %s\", fullPath);\n      return this.scanDirectory(fullPath);\n    }\n\n    return this.scanFile(fullPath);\n  }\n\n\n  /**\n   * Scans a directory recursively, extracting units from supported files while honoring exclusions.\n   */\n  private async scanDirectory(dir: string): Promise<IndexUnit[]> {\n    const out: IndexUnit[] = [];\n    const relDir = this.relPath(dir);\n    const files = await this.listSourceFiles(relDir);\n    for (const relFile of files) {\n      const absFile = path.join(this.root, relFile);\n      const extracted = await this.tryScanSupportedFile(absFile);\n      out.push(...extracted);\n    }\n    return out;\n  }\n\n  /**\n   * Scans a single file and extracts supported units.\n   */\n  private async scanFile(filePath: string): Promise<IndexUnit[]> {\n    return this.tryScanSupportedFile(filePath, true);\n  }\n\n  /**\n   * Extracts units from a supported file.\n   * Optionally throws when the file type is unsupported (used when scanning an explicit file).\n   */\n  private async tryScanSupportedFile(filePath: string, throwOnUnsupported = false): Promise<IndexUnit[]> {\n    const extractor = this.extractors.find(ex => ex.supports(filePath));\n    if (!extractor) {\n      if (throwOnUnsupported) {\n        throw new Error(`Unsupported file type: ${filePath}`);\n      }\n      return [];\n    }\n    const rel = this.relPath(filePath);\n    if (await this.shouldExclude(rel)) {\n      log(\"Skipping excluded file %s\", rel);\n      return [];\n    }\n    const source = await fs.readFile(filePath, \"utf8\");\n    const units = await extractor.extractFromText(rel, source);\n    log(\"Extracted %d units from %s\", units.length, rel);\n    return units.map(unit => ({\n      ...unit,\n      filePath: rel,\n      embedding: undefined,\n    }));\n  }\n\n  /**\n   * Converts an absolute path to a repo-relative, normalized (POSIX-style) path.\n   * This keeps paths stable across platforms and consistent in the index/DB.\n   */\n  private relPath(absPath: string): string {\n    return this.normalizeRelPath(upath.relative(this.root, absPath));\n  }\n\n  /**\n   * Returns true if a repo-relative path matches any configured exclusion glob.\n   */\n  private async shouldExclude(relPath: string): Promise<boolean> {\n    const config = await this.loadConfig();\n    const ignoreMatcher = await this.gitignore.buildMatcher(config);\n    return ignoreMatcher.ignores(this.normalizeRelPath(relPath));\n  }\n\n  private async loadConfig(): Promise<DryConfig> {\n    return await configStore.get(this.root);\n  }\n\n  /**\n   * Normalizes repo-relative paths and strips leading \"./\" to keep matcher inputs consistent.\n   */\n  private normalizeRelPath(relPath: string): string {\n    const normalized = upath.normalizeTrim(relPath);\n    return normalized.startsWith(\"./\") ? normalized.slice(2) : normalized;\n  }\n\n  private async resolveTarget(dirPath: string): Promise<{ fullPath: string; baseRel: string; stat: Stats; }> {\n    const fullPath = path.isAbsolute(dirPath) ? dirPath : path.join(this.root, dirPath);\n    const stat = await fs.stat(fullPath).catch(() => null);\n    if (!stat) {\n      throw new Error(`Path not found: ${fullPath}`);\n    }\n    const baseRel = this.relPath(fullPath);\n    log(\"Listing source files under %s\", fullPath);\n    return { fullPath, baseRel, stat };\n  }\n\n  private async filterSingleFile(baseRel: string, ignoreMatcher: Ignore): Promise<string[]> {\n    const relFile = this.normalizeRelPath(baseRel);\n    if (ignoreMatcher.ignores(relFile)) return [];\n    return this.extractors.some((ex) => ex.supports(relFile)) ? [relFile] : [];\n  }\n\n  private async globSourceFiles(baseRel: string): Promise<string[]> {\n    const pattern = baseRel ? `${baseRel.replace(/\\\\/g, \"/\")}/**/*` : \"**/*\";\n    const matches = await glob(pattern, {\n      cwd: this.root,\n      dot: false,\n      nodir: true,\n    });\n    return matches.map((p: string) => this.normalizeRelPath(p));\n  }\n\n  private filterSupportedFiles(relPaths: string[], ignoreMatcher: Ignore): string[] {\n    return relPaths\n      .filter((relPath: string) => !ignoreMatcher.ignores(relPath))\n      .filter((relPath: string) => this.extractors.some((ex) => ex.supports(relPath)));\n  }\n}\n","import crypto from \"node:crypto\";\nimport Parser from \"tree-sitter\";\nimport Java from \"tree-sitter-java\";\nimport { LanguageExtractor } from \"./LanguageExtractor\";\nimport { IndexUnit, IndexUnitType } from \"../types\";\nimport { indexConfig } from \"../config/indexConfig\";\nimport { DryConfig } from \"../types\";\nimport { configStore } from \"../config/configStore\";\nimport { BLOCK_HASH_ALGO } from \"../const\";\n\nexport class JavaExtractor implements LanguageExtractor {\n  readonly id = \"java\";\n  readonly exts = [\".java\"];\n\n  private parser: Parser;\n  private readonly repoPath: string;\n  private config?: DryConfig;\n\n  constructor(repoPath: string) {\n    this.repoPath = repoPath;\n    this.parser = new Parser();\n    this.parser.setLanguage(Java);\n  }\n\n  supports(filePath: string): boolean {\n    const lower = filePath.toLowerCase();\n    return this.exts.some((ext) => lower.endsWith(ext));\n  }\n\n  async extractFromText(fileRelPath: string, source: string): Promise<IndexUnit[]> {\n    if (!source.trim()) return [];\n\n    this.config = await configStore.get(this.repoPath);\n\n    const tree = this.parser.parse(source);\n    const units: IndexUnit[] = [];\n\n    const visit = (node: Parser.SyntaxNode, currentClass?: IndexUnit) => {\n      if (this.isClassNode(node)) {\n        const className = this.getClassName(node, source) || \"<anonymous>\";\n        if (this.isDtoClass(node, source, className)) {\n          return;\n        }\n        const startLine = node.startPosition.row;\n        const endLine = node.endPosition.row;\n        const classLength = endLine - startLine;\n        const skipClass = this.shouldSkip(IndexUnitType.CLASS, className, classLength);\n        const classId = this.buildId(IndexUnitType.CLASS, className, startLine, endLine);\n        const code = this.stripComments(this.stripClassBody(node, source));\n        const classUnit: IndexUnit = {\n          id: classId,\n          name: className,\n          filePath: fileRelPath,\n          startLine,\n          endLine,\n          code,\n          unitType: IndexUnitType.CLASS,\n          children: [],\n        };\n        if (!skipClass) {\n          units.push(classUnit);\n        }\n\n        for (let i = 0; i < node.namedChildCount; i++) {\n          const child = node.namedChild(i);\n          if (child) visit(child, skipClass ? undefined : classUnit);\n        }\n        return;\n      }\n\n      if (this.isFunctionNode(node)) {\n        const fnUnit = this.buildFunctionUnit(node, source, fileRelPath, currentClass);\n        const fnLength = fnUnit.endLine - fnUnit.startLine;\n        const bodyNode = this.getFunctionBody(node);\n        const skipFunction = this.shouldSkip(IndexUnitType.FUNCTION, fnUnit.name, fnLength);\n\n        if (skipFunction) {\n          return;\n        }\n\n        units.push(fnUnit);\n\n        if (bodyNode) {\n          const blocks = this.extractBlocks(bodyNode, source, fileRelPath, fnUnit);\n          units.push(...blocks);\n        }\n      }\n\n      for (let i = 0; i < node.namedChildCount; i++) {\n        const child = node.namedChild(i);\n        if (child) visit(child, currentClass);\n      }\n    };\n\n    visit(tree.rootNode);\n\n    //remove duplicates if any\n    return this.removeDuplicates(units);\n  }\n\n  unitLabel(unit: IndexUnit): string | null {\n    if (unit.unitType === IndexUnitType.CLASS) return unit.filePath;\n    if (unit.unitType === IndexUnitType.FUNCTION) return this.canonicalFunctionSignature(unit);\n    if (unit.unitType === IndexUnitType.BLOCK) return this.normalizedBlockHash(unit);\n    return unit.name;\n  }\n\n  private isClassNode(node: Parser.SyntaxNode): boolean {\n    return node.type === \"class_declaration\";\n  }\n\n  private getClassName(node: Parser.SyntaxNode, source: string): string | null {\n    const nameNode = node.childForFieldName?.(\"name\");\n    return nameNode ? source.slice(nameNode.startIndex, nameNode.endIndex) : null;\n  }\n\n  private isFunctionNode(node: Parser.SyntaxNode): boolean {\n    return node.type === \"method_declaration\" || node.type === \"constructor_declaration\";\n  }\n\n  private getFunctionName(node: Parser.SyntaxNode, source: string, parentClass?: IndexUnit): string | null {\n    const nameNode = node.childForFieldName?.(\"name\");\n    const nameText = nameNode ? source.slice(nameNode.startIndex, nameNode.endIndex) : \"<anonymous>\";\n    return parentClass ? `${parentClass.name}.${nameText}` : nameText;\n  }\n\n  private getFunctionBody(node: Parser.SyntaxNode): Parser.SyntaxNode | null {\n    return node.childForFieldName?.(\"body\") ?? null;\n  }\n\n  private isBlockNode(node: Parser.SyntaxNode): boolean {\n    return node.type === \"block\";\n  }\n\n  private getMethodBodiesForClass(node: Parser.SyntaxNode): Parser.SyntaxNode[] {\n    const bodies: Parser.SyntaxNode[] = [];\n    const classBody = node.children.find(child => child.type === \"class_body\");\n    if (!classBody) return bodies;\n    \n    for (let i = 0; i < classBody.namedChildCount; i++) {\n      const child = classBody.namedChild(i);\n      if (!child) continue;\n      if (child.type === \"method_declaration\" || child.type === \"constructor_declaration\") {\n        const body = child.childForFieldName?.(\"body\");\n        if (body) bodies.push(body);\n      }\n    }\n    return bodies;\n  }\n\n  private canonicalFunctionSignature(unit: IndexUnit): string {\n    const arity = this.extractArity(unit.code);\n    return `${unit.name}(arity:${arity})`;\n  }\n\n  private normalizedBlockHash(unit: IndexUnit): string {\n    const normalized = this.normalizeCode(unit.code);\n    return crypto.createHash(BLOCK_HASH_ALGO).update(normalized).digest(\"hex\");\n  }\n\n  private shouldSkip(unitType: IndexUnitType, name: string, lineCount: number): boolean {\n    if (!this.config) {\n      throw new Error(\"Config not loaded before skip evaluation\");\n    }\n    const config = this.config;\n    const minLines = unitType === IndexUnitType.BLOCK\n      ? Math.max(indexConfig.blockMinLines, config.minBlockLines ?? 0)\n      : config.minLines;\n    const belowMin = minLines > 0 && lineCount < minLines;\n    const trivial = unitType === IndexUnitType.FUNCTION && this.isTrivialFunction(name);\n    return belowMin || trivial;\n  }\n\n  private isTrivialFunction(fullName: string): boolean {\n    const simpleName = fullName.split(\".\").pop() || fullName;\n    const isGetter = /^(get|is)[A-Z]/.test(simpleName);\n    const isSetter = /^set[A-Z]/.test(simpleName);\n    return isGetter || isSetter;\n  }\n\n  private isDtoClass(node: Parser.SyntaxNode, source: string, className: string): boolean {\n    const classBody = node.children.find((child) => child.type === \"class_body\");\n    if (!classBody) return false;\n\n    let hasField = false;\n\n    for (let i = 0; i < classBody.namedChildCount; i++) {\n      const child = classBody.namedChild(i);\n      if (!child) continue;\n\n      if (child.type === \"field_declaration\") {\n        hasField = true;\n        continue;\n      }\n\n      if (child.type.includes(\"annotation\")) {\n        continue;\n      }\n\n      if (child.type === \"method_declaration\" || child.type === \"constructor_declaration\") {\n        const simpleName = this.getSimpleFunctionName(child, source);\n        const fullName = `${className}.${simpleName}`;\n        if (!this.isTrivialFunction(fullName)) {\n          return false;\n        }\n        continue;\n      }\n\n      return false;\n    }\n\n    return hasField;\n  }\n\n  private getSimpleFunctionName(node: Parser.SyntaxNode, source: string): string {\n    const nameNode = node.childForFieldName?.(\"name\");\n    return nameNode ? source.slice(nameNode.startIndex, nameNode.endIndex) : \"<anonymous>\";\n  }\n\n  private buildFunctionUnit(\n    node: Parser.SyntaxNode,\n    source: string,\n    file: string,\n    parentClass?: IndexUnit\n  ): IndexUnit {\n    const name = this.getFunctionName(node, source, parentClass) || \"<anonymous>\";\n    const startLine = node.startPosition.row;\n    const endLine = node.endPosition.row;\n    const id = this.buildId(IndexUnitType.FUNCTION, name, startLine, endLine);\n    const unit: IndexUnit = {\n      id,\n      name,\n      filePath: file,\n      startLine,\n      endLine,\n      code: this.stripComments(source.slice(node.startIndex, node.endIndex)),\n      unitType: IndexUnitType.FUNCTION,\n      parentId: parentClass?.id,\n      parent: parentClass,\n    };\n    if (parentClass) {\n      parentClass.children = parentClass.children || [];\n      parentClass.children.push(unit);\n    }\n    return unit;\n  }\n\n  private extractBlocks(\n    bodyNode: Parser.SyntaxNode,\n    source: string,\n    file: string,\n    parentFunction: IndexUnit\n  ): IndexUnit[] {\n    const blocks: IndexUnit[] = [];\n\n    const visit = (n: Parser.SyntaxNode) => {\n      if (this.isBlockNode(n)) {\n        const startLine = n.startPosition.row;\n        const endLine = n.endPosition.row;\n        const lineCount = endLine - startLine;\n        if (this.shouldSkip(IndexUnitType.BLOCK, parentFunction.name, lineCount)) {\n          return;\n        }\n        if (lineCount >= indexConfig.blockMinLines) {\n          const id = this.buildId(IndexUnitType.BLOCK, parentFunction.name, startLine, endLine);\n          const blockUnit: IndexUnit = {\n            id,\n            name: parentFunction.name,\n            filePath: file,\n            startLine,\n            endLine,\n            code: this.stripComments(source.slice(n.startIndex, n.endIndex)),\n            unitType: IndexUnitType.BLOCK,\n            parentId: parentFunction.id,\n            parent: parentFunction,\n          };\n          parentFunction.children = parentFunction.children || [];\n          parentFunction.children.push(blockUnit);\n          blocks.push(blockUnit);\n        }\n      }\n\n      for (let i = 0; i < n.namedChildCount; i++) {\n        const child = n.namedChild(i);\n        if (child) visit(child);\n      }\n    };\n\n    visit(bodyNode);\n    return blocks;\n  }\n\n  private stripClassBody(node: Parser.SyntaxNode, source: string): string {\n    const classStart = node.startIndex;\n    let code = source.slice(classStart, node.endIndex);\n\n    const methodBodies: Array<{ start: number; end: number }> = [];\n    const candidates = this.getMethodBodiesForClass(node);\n\n    for (const body of candidates) {\n      methodBodies.push({ start: body.startIndex - classStart, end: body.endIndex - classStart });\n    }\n\n    methodBodies.sort((a, b) => b.start - a.start);\n    for (const body of methodBodies) {\n      code = code.slice(0, body.start) + \" { }\" + code.slice(body.end);\n    }\n\n    return code;\n  }\n\n  private buildId(type: IndexUnitType, name: string, startLine: number, endLine: number): string {\n    return `${type}:${name}:${startLine}-${endLine}`;\n  }\n\n  private extractArity(code: string): number {\n    const match = code.match(/^[^{]*?\\(([^)]*)\\)/s);\n    if (!match) return 0;\n    const params = match[1]\n      .split(\",\")\n      .map((p) => p.trim())\n      .filter(Boolean);\n    return params.length;\n  }\n\n  private normalizeCode(code: string): string {\n    const withoutBlockComments = code.replace(/\\/\\*[\\s\\S]*?\\*\\//g, \"\");\n    const withoutLineComments = withoutBlockComments.replace(/\\/\\/[^\\n\\r]*/g, \"\");\n    return withoutLineComments.replace(/\\s+/g, \"\");\n  }\n\n  private stripComments(code: string): string {\n    const withoutBlockComments = code.replace(/\\/\\*[\\s\\S]*?\\*\\//g, (match) => match.replace(/[^\\n\\r]/g, \"\"));\n    return withoutBlockComments.replace(/\\/\\/[^\\n\\r]*/g, \"\");\n  }\n\nprivate removeDuplicates(units: IndexUnit[]): IndexUnit[] | PromiseLike<IndexUnit[]> {\n  return Array.from(new Map(units.map(u => [u.id, u])).values());\n}\n}\n\n","export const indexConfig = {\n  blockMinLines: 5,\n  thresholds: {\n    class: 0.88,\n    function: 0.88,\n    block: 0.88,\n  },\n  weights: {\n    class: { self: 1 },\n    function: { self: 0.8, parentClass: 0.2 },\n    block: { self: 0.7, parentFunction: 0.2, parentClass: 0.1 },\n  },\n};\n","import upath from \"upath\";\nimport { DryConfig } from \"../types\";\nimport { ensureDefaultConfig, resolveDryConfig, saveDryConfig } from \"./dryconfig\";\n\nclass ConfigStore {\n  private readonly cache = new Map<string, DryConfig>();\n  private readonly loading = new Map<string, Promise<DryConfig>>();\n\n  async init(repoPath: string): Promise<DryConfig> {\n    const key = this.normalize(repoPath);\n    return this.load(key, repoPath);\n  }\n\n  async get(repoPath: string): Promise<DryConfig> {\n    const key = this.normalize(repoPath);\n    const cached = this.cache.get(key);\n    if (cached) return cached;\n    return this.load(key, repoPath);\n  }\n\n  async refresh(repoPath: string): Promise<DryConfig> {\n    const key = this.normalize(repoPath);\n    this.cache.delete(key);\n    return this.load(key, repoPath);\n  }\n\n  async save(repoPath: string, config: DryConfig): Promise<void> {\n    const key = this.normalize(repoPath);\n    await saveDryConfig(repoPath, config);\n    this.cache.set(key, config);\n  }\n\n  private async load(key: string, repoPath: string): Promise<DryConfig> {\n    const existing = this.loading.get(key);\n    if (existing) return existing;\n\n    const promise = ensureDefaultConfig(repoPath).then(() => resolveDryConfig(repoPath)).then((config) => {\n      this.cache.set(key, config);\n      this.loading.delete(key);\n      return config;\n    }).catch((err) => {\n      this.loading.delete(key);\n      throw err;\n    });\n\n    this.loading.set(key, promise);\n    return promise;\n  }\n\n  private normalize(repoPath: string): string {\n    return upath.normalizeTrim(upath.resolve(repoPath));\n  }\n}\n\nexport const configStore = new ConfigStore();\n","import fs from \"fs/promises\";\nimport upath from \"upath\";\nimport { Validator, Schema } from \"jsonschema\";\nimport { DryConfig } from \"../types\";\n\n// Baseline config used when no file is present; exported so tests and constructors can seed defaults.\nexport const DEFAULT_CONFIG: DryConfig = {\n  excludedPaths: [\n    \"**/test/**\",\n  ],\n  excludedPairs: [],\n  minLines: 3,\n  minBlockLines: 5,\n  threshold: 0.88,\n  embeddingSource: \"http://localhost:11434\",\n  contextLength: 2048,\n};\n\nconst validator = new Validator();\n\nconst partialConfigSchema: Schema = {\n  type: \"object\",\n  properties: {\n    excludedPaths: { type: \"array\", items: { type: \"string\" } },\n    excludedPairs: { type: \"array\", items: { type: \"string\" } },\n    minLines: { type: \"number\" },\n    minBlockLines: { type: \"number\" },\n    threshold: { type: \"number\" },\n    embeddingSource: { type: \"string\" },\n    contextLength: { type: \"number\" },\n  },\n};\n\nconst fullConfigSchema: Schema = {\n  ...partialConfigSchema,\n  required: [\n    \"excludedPaths\",\n    \"excludedPairs\",\n    \"minLines\",\n    \"minBlockLines\",\n    \"threshold\",\n    \"embeddingSource\",\n    \"contextLength\",\n  ],\n};\n\nfunction validateConfig(raw: unknown, schema: Schema, source: string): any {\n  const result = validator.validate(raw, schema);\n  if (!result.valid) {\n    const details = result.errors.map((e) => e.stack).join(\"; \");\n    throw new Error(`${source} config is invalid: ${details}`);\n  }\n  return raw;\n}\n\nasync function readConfigFile(repoPath: string): Promise<Partial<DryConfig>> {\n  const configPath = upath.join(repoPath, \"dryconfig.json\");\n  try {\n    const content = await fs.readFile(configPath, \"utf8\");\n    let parsed: Partial<DryConfig> = {};\n    try {\n      parsed = JSON.parse(content) as Partial<DryConfig>;\n    } catch (parseErr) {\n      throw new Error(`Invalid JSON in ${configPath}: ${(parseErr as Error).message}`);\n    }\n    return parsed;\n  } catch (err: any) {\n    if (err?.code === \"ENOENT\") {\n      return {};\n    }\n    throw err;\n  }\n}\n\n/**\n * Resolves the effective config for a repo using defaults merged with any file config.\n */\nexport async function resolveDryConfig(repoPath: string): Promise<DryConfig> {\n  const fileConfigRaw = await readConfigFile(repoPath);\n  validateConfig(fileConfigRaw, partialConfigSchema, \"Config file\");\n\n  const merged = { ...DEFAULT_CONFIG, ...fileConfigRaw };\n  validateConfig(merged, fullConfigSchema, \"Merged\");\n  return merged as DryConfig;\n}\n\n// Backwards-compatible helper used by existing callers (file + defaults).\nexport async function loadDryConfig(repoPath: string): Promise<DryConfig> {\n  return resolveDryConfig(repoPath);\n}\n\nexport async function saveDryConfig(repoPath: string, config: DryConfig): Promise<void> {\n  const configPath = upath.join(repoPath, \"dryconfig.json\");\n  validateConfig(config, fullConfigSchema, \"Config to save\");\n  await fs.writeFile(configPath, JSON.stringify(config, null, 2), \"utf8\");\n}\n\nexport async function ensureDefaultConfig(repoPath: string): Promise<void> {\n  const configPath = upath.join(repoPath, \"dryconfig.json\");\n  const repoExists = await fs.stat(repoPath).then((s) => s.isDirectory()).catch((err: any) => {\n    if (err?.code === \"ENOENT\") return false;\n    throw err;\n  });\n\n  if (!repoExists) return;\n\n  const exists = await fs.stat(configPath).then(() => true).catch((err: any) => {\n    if (err?.code === \"ENOENT\") return false;\n    throw err;\n  });\n\n  if (!exists) {\n    await saveDryConfig(repoPath, DEFAULT_CONFIG);\n  }\n}\n","import path from \"path\";\nimport fs from \"fs/promises\";\nimport upath from \"upath\";\nimport { glob } from \"glob-gitignore\";\nimport ignore, { Ignore } from \"ignore\";\nimport { DryConfig } from \"./types\";\n\n/**\n * Gitignore helper that builds ignore matchers by combining default rules,\n * repo .gitignore files, and config-driven exclusions.\n */\nexport class Gitignore {\n  private readonly defaultIgnores = [\".git/**\", \".dry/**\"];\n\n  constructor(private readonly root: string) {}\n\n  async buildMatcher(config: DryConfig): Promise<Ignore> {\n    const rules = await this.resolveRules(config);\n    return ignore({ allowRelativePaths: true }).add(rules);\n  }\n\n  private async resolveRules(config: DryConfig): Promise<string[]> {\n    const gitignoreRules = await this.loadGitignoreRules();\n    const configRules = config.excludedPaths || [];\n    return [...this.defaultIgnores, ...gitignoreRules, ...configRules];\n  }\n\n  private async loadGitignoreRules(): Promise<string[]> {\n    const gitignoreFiles = await glob(\"**/.gitignore\", {\n      cwd: this.root,\n      dot: true,\n      nodir: true,\n      ignore: this.defaultIgnores,\n    });\n\n    const rules: string[] = [];\n\n    for (const file of gitignoreFiles) {\n      const absPath = path.join(this.root, file);\n      const dir = upath.normalizeTrim(upath.dirname(file));\n      const content = await fs.readFile(absPath, \"utf8\").catch(() => \"\");\n      const lines = content.split(/\\r?\\n/);\n\n      for (const raw of lines) {\n        const trimmed = raw.trim();\n        if (!trimmed || trimmed.startsWith(\"#\")) continue;\n\n        const negated = trimmed.startsWith(\"!\");\n        const body = negated ? trimmed.slice(1) : trimmed;\n\n        const scoped = this.scopeRule(body, dir);\n        if (!scoped) continue;\n\n        rules.push(negated ? `!${scoped}` : scoped);\n      }\n    }\n\n    return rules;\n  }\n\n  private scopeRule(rule: string, gitignoreDir: string): string | null {\n    const cleaned = rule.replace(/^\\//, \"\");\n    if (!cleaned) return null;\n\n    if (!gitignoreDir || gitignoreDir === \".\") {\n      return cleaned;\n    }\n\n    return upath.normalizeTrim(upath.join(gitignoreDir, cleaned));\n  }\n}\n","import \"reflect-metadata\";\nimport fs from \"fs/promises\";\nimport upath from \"upath\";\nimport { DataSource, Repository, In } from \"typeorm\";\nimport { FileEntity } from \"./entities/FileEntity\";\nimport { IndexUnit } from \"../types\";\nimport { IndexUnitEntity } from \"./entities/IndexUnitEntity\";\n\nexport class DryScanDatabase {\n  private dataSource?: DataSource;\n  private unitRepository?: Repository<IndexUnitEntity>;\n  private fileRepository?: Repository<FileEntity>;\n\n  isInitialized(): boolean {\n    return !!this.dataSource?.isInitialized;\n  }\n\n  async init(dbPath: string): Promise<void> {\n    await fs.mkdir(upath.dirname(dbPath), { recursive: true });\n\n    this.dataSource = new DataSource({\n      type: \"sqlite\",\n      database: dbPath,\n      entities: [IndexUnitEntity, FileEntity],\n      synchronize: true,\n      logging: false,\n    });\n\n    await this.dataSource.initialize();\n    this.unitRepository = this.dataSource.getRepository(IndexUnitEntity);\n    this.fileRepository = this.dataSource.getRepository(FileEntity);\n  }\n\n  async saveUnit(unit: IndexUnit): Promise<void> {\n    await this.saveUnits(unit);\n  }\n\n  async saveUnits(units: IndexUnit | IndexUnit[]): Promise<void> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    const payload = Array.isArray(units) ? units : [units];\n    const BATCH_SIZE = 500;\n    for (let i = 0; i < payload.length; i += BATCH_SIZE) {\n      console.debug(`[DryScanDatabase] Saving units ${i + 1}-${Math.min(i + BATCH_SIZE, payload.length)} of ${payload.length}...`);\n      const batch = payload.slice(i, i + BATCH_SIZE);\n      await this.unitRepository.save(batch);\n    }\n  }\n\n  async getUnit(id: string): Promise<IndexUnit | null> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    return this.unitRepository.findOne({ \n      where: { id },\n      relations: [\"children\", \"parent\"]\n    });\n  }\n\n  async getAllUnits(): Promise<IndexUnit[]> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    return this.unitRepository.find({ relations: [\"children\", \"parent\"] });\n  }\n\n  async updateUnit(unit: IndexUnit): Promise<void> {\n    await this.saveUnits(unit);\n  }\n\n  async updateUnits(units: IndexUnit | IndexUnit[]): Promise<void> {\n    await this.saveUnits(units);\n  }\n\n  /**\n   * Returns total count of indexed units.\n   */\n  async countUnits(): Promise<number> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    return this.unitRepository.count();\n  }\n\n  /**\n   * Removes index units by their file paths.\n   * Used during incremental updates when files change.\n   */\n  async removeUnitsByFilePaths(filePaths: string[]): Promise<void> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    await this.unitRepository.delete({ filePath: In(filePaths) });\n  }\n\n  /**\n   * Saves file metadata (path, checksum, mtime) to track changes.\n   */\n  async saveFile(file: FileEntity): Promise<void> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    await this.fileRepository.save(file);\n  }\n\n  /**\n   * Saves multiple file metadata entries.\n   */\n  async saveFiles(files: FileEntity[]): Promise<void> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    await this.fileRepository.save(files);\n  }\n\n  /**\n   * Gets file metadata by file path.\n   */\n  async getFile(filePath: string): Promise<FileEntity | null> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    return this.fileRepository.findOne({ where: { filePath } });\n  }\n\n  /**\n   * Gets all tracked files.\n   */\n  async getAllFiles(): Promise<FileEntity[]> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    return this.fileRepository.find();\n  }\n\n  /**\n   * Removes file metadata entries by file paths.\n   * Used when files are deleted from repository.\n   */\n  async removeFilesByFilePaths(filePaths: string[]): Promise<void> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    await this.fileRepository.delete({ filePath: In(filePaths) });\n  }\n\n  async close(): Promise<void> {\n    if (this.dataSource?.isInitialized) {\n      await this.dataSource.destroy();\n    }\n  }\n}\n","import { Entity, PrimaryColumn, Column } from \"typeorm\";\n\n/**\n * Represents a tracked source file in the repository.\n * Used to detect changes via checksum and mtime for incremental updates.\n */\n@Entity(\"files\")\nexport class FileEntity {\n  /**\n   * Relative path to the file from repository root.\n   * Used as primary key for uniqueness.\n   */\n  @PrimaryColumn(\"text\")\n  filePath!: string;\n\n  /**\n   * MD5 checksum of file content.\n   * Used to detect content changes.\n   */\n  @Column(\"text\")\n  checksum!: string;\n\n  /**\n   * Last modification time in milliseconds since epoch.\n   * Used as fast sanity check before computing checksum.\n   */\n  @Column(\"integer\")\n  mtime!: number;\n}\n","import {\n  Column,\n  Entity,\n  JoinColumn,\n  ManyToOne,\n  OneToMany,\n  PrimaryColumn,\n  RelationId,\n} from \"typeorm\";\nimport { IndexUnit, IndexUnitType } from \"../../types\";\n\n@Entity(\"index_units\")\nexport class IndexUnitEntity implements IndexUnit {\n  @PrimaryColumn(\"text\")\n  id!: string;\n\n  @Column(\"text\")\n  name!: string;\n\n  @Column(\"text\")\n  filePath!: string;\n\n  @Column(\"integer\")\n  startLine!: number;\n\n  @Column(\"integer\")\n  endLine!: number;\n\n  @Column(\"text\")\n  code!: string;\n\n  @Column(\"text\")\n  unitType!: IndexUnitType;\n\n  @ManyToOne(() => IndexUnitEntity, (unit) => unit.children, {\n    nullable: true,\n    onDelete: \"CASCADE\",\n  })\n  @JoinColumn({ name: \"parent_id\" })\n  parent?: IndexUnitEntity | null;\n\n  @RelationId((unit: IndexUnitEntity) => unit.parent)\n  parentId?: string | null;\n\n  @OneToMany(() => IndexUnitEntity, (unit) => unit.parent, { nullable: true })\n  children?: IndexUnitEntity[];\n\n  @Column(\"simple-array\", { nullable: true })\n  embedding?: number[] | null;\n}\n","import path from \"path\";\nimport fs from \"fs/promises\";\nimport { DryScanServiceDeps } from \"./types\";\nimport { ExclusionService } from \"./ExclusionService\";\nimport { IndexUnit } from \"../types\";\nimport { EmbeddingService } from \"./EmbeddingService\";\nimport { FileEntity } from \"../db/entities/FileEntity\";\nimport { IndexUnitExtractor } from \"../IndexUnitExtractor\";\n\nexport interface InitOptions {\n  skipEmbeddings?: boolean;\n}\n\nexport class RepositoryInitializer {\n  constructor(\n    private readonly deps: DryScanServiceDeps,\n    private readonly exclusionService: ExclusionService\n  ) {}\n\n  async init(options?: InitOptions): Promise<void> {\n    const extractor = this.deps.extractor;\n\n    console.log(\"[DryScan] Phase 1/3: Extracting code units...\");\n    await this.initUnits(extractor);\n    console.log(\"[DryScan] Phase 2/3: Computing embeddings (may be slow)...\");\n    await this.computeEmbeddings(options?.skipEmbeddings === true);\n    console.log(\"[DryScan] Phase 3/3: Tracking files...\");\n    await this.trackFiles(extractor);\n    await this.exclusionService.cleanupExcludedFiles();\n    console.log(\"[DryScan] Initialization phases complete.\");\n  }\n\n  private async initUnits(extractor: IndexUnitExtractor): Promise<void> {\n    const units = await extractor.scan(this.deps.repoPath);\n    console.log(`[DryScan] Extracted ${units.length} index units.`);\n    await this.deps.db.saveUnits(units);\n  }\n\n  private async computeEmbeddings(skipEmbeddings: boolean): Promise<void> {\n    if (skipEmbeddings) {\n      console.log(\"[DryScan] Skipping embedding computation by request.\");\n      return;\n    }\n    const allUnits: IndexUnit[] = await this.deps.db.getAllUnits();\n    const total = allUnits.length;\n    console.log(`[DryScan] Computing embeddings for ${total} units...`);\n\n    const updated: IndexUnit[] = [];\n    const progressInterval = Math.max(1, Math.ceil(total / 10));\n    const embeddingService = new EmbeddingService(this.deps.repoPath);\n\n    for (let i = 0; i < total; i++) {\n      const unit = allUnits[i];\n      try {\n        const enriched = await embeddingService.addEmbedding(unit);\n        updated.push(enriched);\n      } catch (err: any) {\n        console.error(\n          `[DryScan] Embedding failed for ${unit.filePath} (${unit.name}): ${err?.message || err}`\n        );\n        throw err;\n      }\n\n      const completed = i + 1;\n      if (completed === total || completed % progressInterval === 0) {\n        const pct = Math.floor((completed / total) * 100);\n        console.log(`[DryScan] Embeddings ${completed}/${total} (${pct}%)`);\n      }\n    }\n\n    await this.deps.db.updateUnits(updated);\n  }\n\n  private async trackFiles(extractor: IndexUnitExtractor): Promise<void> {\n    const allFunctions = await extractor.listSourceFiles(this.deps.repoPath);\n    const fileEntities: FileEntity[] = [];\n\n    for (const relPath of allFunctions) {\n      const fullPath = path.join(this.deps.repoPath, relPath);\n      const stat = await fs.stat(fullPath);\n      const checksum = await extractor.computeChecksum(fullPath);\n\n      const fileEntity = new FileEntity();\n      fileEntity.filePath = relPath;\n      fileEntity.checksum = checksum;\n      fileEntity.mtime = stat.mtimeMs;\n      fileEntities.push(fileEntity);\n    }\n\n    await this.deps.db.saveFiles(fileEntities);\n    console.log(`[DryScan] Tracked ${fileEntities.length} files.`);\n  }\n}","import debug from \"debug\";\nimport { OllamaEmbeddings } from \"@langchain/ollama\";\nimport { HuggingFaceInferenceEmbeddings } from \"@langchain/community/embeddings/hf\";\nimport { IndexUnit } from \"../types\";\nimport { configStore } from \"../config/configStore\";\n\nconst log = debug(\"DryScan:EmbeddingService\");\n\n// Model names for each provider\nconst OLLAMA_MODEL = \"qwen3-embedding:0.6b\";\nconst HUGGINGFACE_MODEL = \"Qwen/Qwen3-Embedding-0.6B\";\n\nexport class EmbeddingService {\n    constructor(private readonly repoPath: string) { }\n\n    /**\n     * Generates an embedding for the given index unit using the configured provider.\n     * Skips embedding if code exceeds the configured context length.\n     */\n    async addEmbedding(fn: IndexUnit): Promise<IndexUnit> {\n        const config = await configStore.get(this.repoPath);\n        const maxContext = config?.contextLength ?? 2048;\n        if (fn.code.length > maxContext) {\n            log(\n                \"Skipping embedding for %s (code length %d exceeds context %d)\",\n                fn.id,\n                fn.code.length,\n                maxContext\n            );\n            return { ...fn, embedding: null };\n        }\n\n        const source = config.embeddingSource;\n        if (!source) {\n            const message = `Embedding source is not configured for repository at ${this.repoPath}`;\n            log(message);\n            throw new Error(message);\n        }\n\n        const embeddings = this.buildProvider(source);\n        const embedding = await embeddings.embedQuery(fn.code);\n        return { ...fn, embedding };\n    }\n\n    /**\n     * Builds the embedding provider based on the source configuration.\n     * - URL (http/https): Uses Ollama with \"embeddinggemma\" model\n     * - \"huggingface\": Uses HuggingFace Inference API with \"embeddinggemma-300m\" model\n     */\n    private buildProvider(source: string) {\n        // HuggingFace Inference API\n        if (source.toLowerCase() === \"huggingface\") {\n            log(\"Using HuggingFace Inference with model: %s\", HUGGINGFACE_MODEL);\n            return new HuggingFaceInferenceEmbeddings({\n                model: HUGGINGFACE_MODEL,\n                provider: \"hf-inference\",\n            });\n        }\n\n        // Ollama keyword or direct URL\n        const ollamaBaseUrl = this.resolveOllamaBaseUrl(source);\n        if (ollamaBaseUrl !== null) {\n            log(\"Using Ollama%s with model: %s\", ollamaBaseUrl ? ` at ${ollamaBaseUrl}` : \"\", OLLAMA_MODEL);\n            return new OllamaEmbeddings({ model: OLLAMA_MODEL, ...(ollamaBaseUrl && { baseUrl: ollamaBaseUrl }) });\n        }\n\n        const message = `Unsupported embedding source: ${source || \"(empty)\"}. Use \"huggingface\" or an Ollama URL.`;\n        log(message);\n        throw new Error(message);\n    }\n\n    /**\n     * Returns the Ollama base URL if source is an HTTP URL, undefined if source is \"ollama\" (use default),\n     * or null if source is not an Ollama provider at all.\n     */\n    private resolveOllamaBaseUrl(source: string): string | undefined | null {\n        if (/^https?:\\/\\//i.test(source)) return source;\n        if (source.toLowerCase() === \"ollama\") return undefined;\n        return null;\n    }\n}","import debug from \"debug\";\nimport { DryScanServiceDeps } from \"./types\";\nimport { ExclusionService } from \"./ExclusionService\";\nimport { performIncrementalUpdate } from \"../DryScanUpdater\";\nimport { DuplicationCache } from \"./DuplicationCache\";\n\nconst log = debug(\"DryScan:UpdateService\");\n\nexport class UpdateService {\n  constructor(\n    private readonly deps: DryScanServiceDeps,\n    private readonly exclusionService: ExclusionService\n  ) {}\n\n  async updateIndex(): Promise<void> {\n    const extractor = this.deps.extractor;\n    const cache = DuplicationCache.getInstance();\n\n    try {\n      const changeSet = await performIncrementalUpdate(this.deps.repoPath, extractor, this.deps.db);\n      await this.exclusionService.cleanupExcludedFiles();\n      await cache.invalidate([...changeSet.changed, ...changeSet.deleted]);\n    } catch (err) {\n      log(\"Error during index update:\", err);\n      throw err;\n    }\n  }\n}","import path from \"path\";\nimport fs from \"fs/promises\";\nimport debug from \"debug\";\nimport { IndexUnit } from \"./types\";\nimport { IndexUnitExtractor } from \"./IndexUnitExtractor\";\nimport { DryScanDatabase } from \"./db/DryScanDatabase\";\nimport { FileEntity } from \"./db/entities/FileEntity\";\nimport { EmbeddingService } from \"./services/EmbeddingService\";\n\nconst log = debug(\"DryScan:Updater\");\n\n/**\n * DryScan Updater Module\n * \n * This module contains all incremental update logic for DryScan.\n * Separated from DryScan.ts to keep that file focused on core operations.\n * \n * Represents the result of change detection.\n * Categorizes files into added, changed, deleted, and unchanged.\n */\nexport interface FileChangeSet {\n  added: string[];\n  changed: string[];\n  deleted: string[];\n  unchanged: string[];\n}\n\n/**\n * Detects which files have been added, changed, or deleted since last scan.\n * Uses mtime as fast check, then checksum for verification.\n * \n * @param repoPath - Root path of the repository\n * @param extractor - Index unit extractor instance for file operations\n * @param db - Database instance for retrieving tracked files\n * @returns Change set with categorized file paths\n */\nexport async function detectFileChanges(\n  repoPath: string,\n  extractor: IndexUnitExtractor,\n  db: DryScanDatabase\n): Promise<FileChangeSet> {\n  // Get current files in repository\n  const currentFiles = await extractor.listSourceFiles(repoPath);\n  const currentFileSet = new Set(currentFiles);\n\n  // Get tracked files from database\n  const trackedFiles = await db.getAllFiles();\n  const trackedFileMap = new Map(trackedFiles.map(f => [f.filePath, f]));\n\n  const added: string[] = [];\n  const changed: string[] = [];\n  const unchanged: string[] = [];\n\n  // Check each current file\n  for (const filePath of currentFiles) {\n    const tracked = trackedFileMap.get(filePath);\n    \n    if (!tracked) {\n      // New file\n      added.push(filePath);\n      continue;\n    }\n\n    // Check if file changed using mtime first (fast check)\n    const fullPath = path.join(repoPath, filePath);\n    const stat = await fs.stat(fullPath);\n    \n    if (stat.mtimeMs !== tracked.mtime) {\n      // Mtime changed, verify with checksum\n      const currentChecksum = await extractor.computeChecksum(fullPath);\n      if (currentChecksum !== tracked.checksum) {\n        changed.push(filePath);\n      } else {\n        // Mtime changed but content same\n        unchanged.push(filePath);\n      }\n    } else {\n      unchanged.push(filePath);\n    }\n  }\n\n  // Find deleted files\n  const deleted = trackedFiles\n    .map(f => f.filePath)\n    .filter(fp => !currentFileSet.has(fp));\n\n  return { added, changed, deleted, unchanged };\n}\n\n/**\n * Extracts index units from a list of files.\n * Used during incremental updates.\n * \n * @param filePaths - Array of relative file paths to extract from\n * @param extractor - Index unit extractor instance\n * @returns Array of extracted units\n */\nexport async function extractUnitsFromFiles(\n  filePaths: string[],\n  extractor: IndexUnitExtractor\n): Promise<IndexUnit[]> {\n  const allUnits: IndexUnit[] = [];\n  \n  for (const relPath of filePaths) {\n    const functions = await extractor.scan(relPath);\n    allUnits.push(...functions);\n  }\n  \n  return allUnits;\n}\n\n/**\n * Updates file tracking metadata after processing changes.\n * Removes deleted files, updates changed files, adds new files.\n * \n * @param changeSet - Set of file changes to apply\n * @param repoPath - Root path of the repository\n * @param extractor - Index unit extractor for checksum computation\n * @param db - Database instance for file tracking\n */\nexport async function updateFileTracking(\n  changeSet: FileChangeSet,\n  repoPath: string,\n  extractor: IndexUnitExtractor,\n  db: DryScanDatabase\n): Promise<void> {\n  // Remove deleted files\n  if (changeSet.deleted.length > 0) {\n    if (typeof (db as any).removeFilesByFilePaths === \"function\") {\n      await (db as any).removeFilesByFilePaths(changeSet.deleted);\n    } else if (typeof (db as any).removeFiles === \"function\") {\n      await (db as any).removeFiles(changeSet.deleted);\n    }\n  }\n\n  // Create file entities for new and changed files\n  const filesToTrack = [...changeSet.added, ...changeSet.changed];\n  if (filesToTrack.length > 0) {\n    const fileEntities: FileEntity[] = [];\n    \n    for (const relPath of filesToTrack) {\n      const fullPath = path.join(repoPath, relPath);\n      const stat = await fs.stat(fullPath);\n      const checksum = await extractor.computeChecksum(fullPath);\n      \n      const fileEntity = new FileEntity();\n      fileEntity.filePath = relPath;\n      fileEntity.checksum = checksum;\n      fileEntity.mtime = stat.mtimeMs;\n      \n      fileEntities.push(fileEntity);\n    }\n    \n    await db.saveFiles(fileEntities);\n  }\n}\n\n/**\n * Performs incremental update of the DryScan index.\n * Detects file changes and reprocesses only affected files.\n * \n * @param repoPath - Root path of the repository\n * @param extractor - Index unit extractor instance\n * @param db - Database instance (must be initialized)\n */\nexport async function performIncrementalUpdate(\n  repoPath: string,\n  extractor: IndexUnitExtractor,\n  db: DryScanDatabase,\n): Promise<FileChangeSet> {\n  log(\"Starting incremental update\");\n  const embeddingService = new EmbeddingService(repoPath);\n  \n  // Step 1: Detect changes\n  const changeSet = await detectFileChanges(repoPath, extractor, db);\n  \n  if (changeSet.changed.length === 0 && \n      changeSet.added.length === 0 && \n      changeSet.deleted.length === 0) {\n    log(\"No changes detected. Index is up to date.\");\n    return changeSet;\n  }\n\n  log(`Changes detected: ${changeSet.added.length} added, ${changeSet.changed.length} changed, ${changeSet.deleted.length} deleted`);\n\n  // Step 2: Remove old data for changed/deleted files\n  const filesToRemove = [...changeSet.changed, ...changeSet.deleted];\n  if (filesToRemove.length > 0) {\n      await db.removeUnitsByFilePaths(filesToRemove);\n      log(`Removed units from ${filesToRemove.length} files`);\n  }\n\n  // Step 3: Extract functions from new/changed files\n  const filesToProcess = [...changeSet.added, ...changeSet.changed];\n  if (filesToProcess.length > 0) {\n    const newUnits = await extractUnitsFromFiles(filesToProcess, extractor);\n      await db.saveUnits(newUnits);\n      log(`Extracted and saved ${newUnits.length} units from ${filesToProcess.length} files`);\n\n    // Step 4: Recompute embeddings for affected units only\n    const total = newUnits.length;\n    if (total > 0) {\n      log(`Recomputing embeddings for ${total} units`);\n      const progressInterval = Math.max(1, Math.ceil(total / 10));\n      const updatedWithEmbeddings = [] as IndexUnit[];\n\n      for (let i = 0; i < total; i++) {\n        const unit = newUnits[i];\n        try {\n          const enriched = await embeddingService.addEmbedding(unit);\n          updatedWithEmbeddings.push(enriched);\n        } catch (err: any) {\n          console.error(\n            `[DryScan] embedding failed for ${unit.filePath} (${unit.name}): ${err?.message || err}`\n          );\n          throw err;\n        }\n\n        const completed = i + 1;\n        if (completed === total || completed % progressInterval === 0) {\n          const pct = Math.floor((completed / total) * 100);\n          console.log(`[DryScan] Incremental embeddings ${completed}/${total} (${pct}%)`);\n        }\n      }\n\n      await db.updateUnits(updatedWithEmbeddings);\n      log(`Recomputed embeddings for ${updatedWithEmbeddings.length} units`);\n    }\n  }\n\n  // Step 5: Update file tracking\n  await updateFileTracking(changeSet, repoPath, extractor, db);\n  log(\"Incremental update complete\");\n\n  return changeSet;\n}\n","import { DuplicateGroup } from \"../types\";\n\n/**\n * In-memory cache for duplicate comparison scores.\n * Stores a global map of comparison keys and a per-file index for fast invalidation.\n */\nexport class DuplicationCache {\n  private static instance: DuplicationCache | null = null;\n\n  private readonly comparisons = new Map<string, number>();\n  private readonly fileIndex = new Map<string, Set<string>>();\n  private initialized = false;\n\n  static getInstance(): DuplicationCache {\n    if (!DuplicationCache.instance) {\n      DuplicationCache.instance = new DuplicationCache();\n    }\n    return DuplicationCache.instance;\n  }\n\n  /**\n   * Updates the cache with fresh duplicate groups. Not awaited by callers to avoid blocking.\n   */\n  async update(groups: DuplicateGroup[]): Promise<void> {\n    if (!groups) return;\n\n    for (const group of groups) {\n      const key = this.makeKey(group.left.id, group.right.id);\n      this.comparisons.set(key, group.similarity);\n      this.addKeyForFile(group.left.filePath, key);\n      this.addKeyForFile(group.right.filePath, key);\n    }\n\n    this.initialized = this.initialized || groups.length > 0;\n  }\n\n  /**\n   * Retrieves a cached similarity if present and valid for both file paths.\n   * Returns null when the cache has not been initialized or when the pair is missing.\n   */\n  get(leftId: string, rightId: string, leftFilePath: string, rightFilePath: string): number | null {\n    if (!this.initialized) return null;\n\n    const key = this.makeKey(leftId, rightId);\n    if (!this.fileHasKey(leftFilePath, key) || !this.fileHasKey(rightFilePath, key)) {\n      return null;\n    }\n\n    const value = this.comparisons.get(key);\n    return typeof value === \"number\" ? value : null;\n  }\n\n  /**\n   * Invalidates all cached comparisons involving the provided file paths.\n   */\n  async invalidate(paths: string[]): Promise<void> {\n    if (!this.initialized || !paths || paths.length === 0) return;\n\n    const unique = new Set(paths);\n    for (const filePath of unique) {\n      const keys = this.fileIndex.get(filePath);\n      if (!keys) continue;\n\n      for (const key of keys) {\n        this.comparisons.delete(key);\n        for (const [otherPath, otherKeys] of this.fileIndex.entries()) {\n          if (otherKeys.delete(key) && otherKeys.size === 0) {\n            this.fileIndex.delete(otherPath);\n          }\n        }\n      }\n\n      this.fileIndex.delete(filePath);\n    }\n\n    if (this.comparisons.size === 0) {\n      this.initialized = false;\n    }\n  }\n\n  /**\n   * Clears all cached data. Intended for test setup.\n   */\n  clear(): void {\n    this.comparisons.clear();\n    this.fileIndex.clear();\n    this.initialized = false;\n  }\n\n  private addKeyForFile(filePath: string, key: string): void {\n    const current = this.fileIndex.get(filePath) ?? new Set<string>();\n    current.add(key);\n    this.fileIndex.set(filePath, current);\n  }\n\n  private fileHasKey(filePath: string, key: string): boolean {\n    const keys = this.fileIndex.get(filePath);\n    return keys ? keys.has(key) : false;\n  }\n\n  private makeKey(leftId: string, rightId: string): string {\n    return [leftId, rightId].sort().join(\"::\");\n  }\n}\n","import debug from \"debug\";\nimport shortUuid from \"short-uuid\";\nimport { cosineSimilarity } from \"@langchain/core/utils/math\";\nimport { DryScanServiceDeps } from \"./types\";\nimport { DuplicateAnalysisResult, DuplicateGroup, DuplicationScore, IndexUnit, IndexUnitType } from \"../types\";\nimport { indexConfig } from \"../config/indexConfig\";\nimport { DryConfig } from \"../types\";\nimport { DuplicationCache } from \"./DuplicationCache\";\n\nconst log = debug(\"DryScan:DuplicateService\");\n\nexport class DuplicateService {\n  private config?: DryConfig;\n  private readonly cache = DuplicationCache.getInstance();\n\n  constructor(private readonly deps: DryScanServiceDeps) {}\n\n  async findDuplicates(config: DryConfig): Promise<DuplicateAnalysisResult> {\n    this.config = config;\n    const allUnits = await this.deps.db.getAllUnits();\n    if (allUnits.length < 2) {\n      const score = this.computeDuplicationScore([], allUnits);\n      return { duplicates: [], score };\n    }\n\n    const thresholds = this.resolveThresholds(config.threshold);\n    const duplicates = this.computeDuplicates(allUnits, thresholds);\n    const filteredDuplicates = duplicates.filter((group) => !this.isGroupExcluded(group));\n    log(\"Found %d duplicate groups\", filteredDuplicates.length);\n\n    // Update cache asynchronously; no need to block the main flow.\n    this.cache.update(filteredDuplicates).catch((err) => log(\"Cache update failed: %O\", err));\n\n    const score = this.computeDuplicationScore(filteredDuplicates, allUnits);\n    return { duplicates: filteredDuplicates, score };\n  }\n\n  private resolveThresholds(functionThreshold?: number): { function: number; block: number; class: number } {\n    const defaults = indexConfig.thresholds;\n    const clamp = (value: number) => Math.min(1, Math.max(0, value));\n\n    const base = functionThreshold ?? defaults.function;\n    const blockOffset = defaults.block - defaults.function;\n    const classOffset = defaults.class - defaults.function;\n\n    const functionThresholdValue = clamp(base);\n    return {\n      function: functionThresholdValue,\n      block: clamp(functionThresholdValue + blockOffset),\n      class: clamp(functionThresholdValue + classOffset),\n    };\n  }\n\n  private computeDuplicates(\n    units: IndexUnit[],\n    thresholds: { function: number; block: number; class: number }\n  ): DuplicateGroup[] {\n    const duplicates: DuplicateGroup[] = [];\n    const byType = new Map<IndexUnitType, IndexUnit[]>();\n\n    for (const unit of units) {\n      const list = byType.get(unit.unitType) ?? [];\n      list.push(unit);\n      byType.set(unit.unitType, list);\n    }\n\n    for (const [type, typedUnits] of byType.entries()) {\n      const threshold = this.getThreshold(type, thresholds);\n\n      for (let i = 0; i < typedUnits.length; i++) {\n        for (let j = i + 1; j < typedUnits.length; j++) {\n          const left = typedUnits[i];\n          const right = typedUnits[j];\n\n          if (this.shouldSkipComparison(left, right)) continue;\n\n          const cached = this.cache.get(left.id, right.id, left.filePath, right.filePath);\n          let similarity: number | null = null;\n\n          if (cached !== null) {\n            similarity = cached;\n          } else {\n            if (!left.embedding || !right.embedding) continue;\n            similarity = this.computeWeightedSimilarity(left, right);\n          }\n\n          if (similarity === null) continue;\n\n          if (similarity >= threshold) {\n            const exclusionString = this.deps.pairing.pairKeyForUnits(left, right);\n            if (!exclusionString) continue;\n\n            duplicates.push({\n              id: `${left.id}::${right.id}`,\n              similarity,\n              shortId: shortUuid.generate(),\n              exclusionString,\n              left: {\n                id: left.id,\n                name: left.name,\n                filePath: left.filePath,\n                startLine: left.startLine,\n                endLine: left.endLine,\n                code: left.code,\n                unitType: left.unitType,\n              },\n              right: {\n                id: right.id,\n                name: right.name,\n                filePath: right.filePath,\n                startLine: right.startLine,\n                endLine: right.endLine,\n                code: right.code,\n                unitType: right.unitType,\n              },\n            });\n          }\n        }\n      }\n    }\n\n    return duplicates.sort((a, b) => b.similarity - a.similarity);\n  }\n\n  private isGroupExcluded(group: DuplicateGroup): boolean {\n    const config = this.config;\n    if (!config || !config.excludedPairs || config.excludedPairs.length === 0) return false;\n    const key = this.deps.pairing.pairKeyForUnits(group.left, group.right);\n    if (!key) return false;\n    const actual = this.deps.pairing.parsePairKey(key);\n    if (!actual) return false;\n    return config.excludedPairs.some((entry) => {\n      const parsed = this.deps.pairing.parsePairKey(entry);\n      return parsed ? this.deps.pairing.pairKeyMatches(actual, parsed) : false;\n    });\n  }\n\n  private getThreshold(type: IndexUnitType, thresholds: { function: number; block: number; class: number }): number {\n    if (type === IndexUnitType.CLASS) return thresholds.class;\n    if (type === IndexUnitType.BLOCK) return thresholds.block;\n    return thresholds.function;\n  }\n\n  private computeWeightedSimilarity(left: IndexUnit, right: IndexUnit): number {\n    const selfSimilarity = this.similarityWithFallback(left, right);\n\n    if (left.unitType === IndexUnitType.CLASS) {\n      return selfSimilarity * indexConfig.weights.class.self;\n    }\n\n    if (left.unitType === IndexUnitType.FUNCTION) {\n      const weights = indexConfig.weights.function;\n      const hasParentClass = !!this.findParentOfType(left, IndexUnitType.CLASS) && !!this.findParentOfType(right, IndexUnitType.CLASS);\n      const parentClassSimilarity = hasParentClass ? this.parentSimilarity(left, right, IndexUnitType.CLASS) : 0;\n\n      // Re-normalize weights when parent context is missing, so standalone units aren't penalized.\n      const totalWeight = weights.self + (hasParentClass ? weights.parentClass : 0);\n      return ((weights.self * selfSimilarity) + (hasParentClass ? (weights.parentClass * parentClassSimilarity) : 0)) / totalWeight;\n    }\n\n    const weights = indexConfig.weights.block;\n    const hasParentFunction = !!this.findParentOfType(left, IndexUnitType.FUNCTION) && !!this.findParentOfType(right, IndexUnitType.FUNCTION);\n    const hasParentClass = !!this.findParentOfType(left, IndexUnitType.CLASS) && !!this.findParentOfType(right, IndexUnitType.CLASS);\n    const parentFuncSim = hasParentFunction ? this.parentSimilarity(left, right, IndexUnitType.FUNCTION) : 0;\n    const parentClassSim = hasParentClass ? this.parentSimilarity(left, right, IndexUnitType.CLASS) : 0;\n\n    // Re-normalize weights when some parent context is missing.\n    const totalWeight =\n      weights.self +\n      (hasParentFunction ? weights.parentFunction : 0) +\n      (hasParentClass ? weights.parentClass : 0);\n\n    return (\n      (weights.self * selfSimilarity) +\n      (hasParentFunction ? (weights.parentFunction * parentFuncSim) : 0) +\n      (hasParentClass ? (weights.parentClass * parentClassSim) : 0)\n    ) / totalWeight;\n  }\n\n  private parentSimilarity(left: IndexUnit, right: IndexUnit, targetType: IndexUnitType): number {\n    const leftParent = this.findParentOfType(left, targetType);\n    const rightParent = this.findParentOfType(right, targetType);\n    if (!leftParent || !rightParent) return 0;\n    return this.similarityWithFallback(leftParent, rightParent);\n  }\n\n  private similarityWithFallback(left: IndexUnit, right: IndexUnit): number {\n    const leftHasEmbedding = this.hasVector(left);\n    const rightHasEmbedding = this.hasVector(right);\n\n    if (leftHasEmbedding && rightHasEmbedding) {\n      return cosineSimilarity([left.embedding as number[]], [right.embedding as number[]])[0][0];\n    }\n\n    return this.childSimilarity(left, right);\n  }\n\n  private childSimilarity(left: IndexUnit, right: IndexUnit): number {\n    const leftChildren = left.children ?? [];\n    const rightChildren = right.children ?? 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rightLines) / 2;\n      return sum + group.similarity * avgLines;\n    }, 0);\n\n    const score = (weightedDuplicateLines / totalLines) * 100;\n    const grade = this.getScoreGrade(score);\n\n    return {\n      score,\n      grade,\n      totalLines,\n      duplicateLines: Math.round(weightedDuplicateLines),\n      duplicateGroups: duplicates.length,\n    };\n  }\n\n  private calculateTotalLines(units: IndexUnit[]): number {\n    return units.reduce((sum, unit) => {\n      const lines = unit.endLine - unit.startLine + 1;\n      return sum + lines;\n    }, 0);\n  }\n\n  private getScoreGrade(score: number): DuplicationScore[\"grade\"] {\n    if (score < 5) return \"Excellent\";\n    if (score < 15) return \"Good\";\n    if (score < 30) return \"Fair\";\n    if (score < 50) return \"Poor\";\n    return \"Critical\";\n  }\n}","import { DryConfig } from \"../types\";\nimport { configStore } from \"../config/configStore\";\nimport { DryScanServiceDeps } from \"./types\";\nimport { IndexUnitType } from \"../types\";\nimport { minimatch } from \"minimatch\";\nimport { ParsedPairKey } from \"./PairingService\";\n\nexport class ExclusionService {\n  private config?: DryConfig;\n\n  constructor(private readonly deps: DryScanServiceDeps) {}\n\n  async cleanupExcludedFiles(): Promise<void> {\n    const config = await this.loadConfig();\n    if (!config.excludedPaths || config.excludedPaths.length === 0) return;\n\n    const units = await this.deps.db.getAllUnits();\n    const files = await this.deps.db.getAllFiles();\n\n    const unitPathsToRemove = new Set<string>();\n    for (const unit of units) {\n      if (this.pathExcluded(unit.filePath)) {\n        unitPathsToRemove.add(unit.filePath);\n      }\n    }\n\n    const filePathsToRemove = new Set<string>();\n    for (const file of files) {\n      if (this.pathExcluded(file.filePath)) {\n        filePathsToRemove.add(file.filePath);\n      }\n    }\n\n    const paths = [...new Set([...unitPathsToRemove, ...filePathsToRemove])];\n    if (paths.length > 0) {\n      await this.deps.db.removeUnitsByFilePaths(paths);\n      await this.deps.db.removeFilesByFilePaths(paths);\n    }\n  }\n\n  async cleanExclusions(): Promise<{ removed: number; kept: number }> {\n    const config = await this.loadConfig();\n    const units = await this.deps.db.getAllUnits();\n\n    const actualPairsByType = {\n      [IndexUnitType.CLASS]: this.buildPairKeys(units, IndexUnitType.CLASS),\n      [IndexUnitType.FUNCTION]: this.buildPairKeys(units, IndexUnitType.FUNCTION),\n      [IndexUnitType.BLOCK]: this.buildPairKeys(units, IndexUnitType.BLOCK),\n    };\n\n    const kept: string[] = [];\n    const removed: string[] = [];\n\n    for (const entry of config.excludedPairs || []) {\n      const parsed = this.deps.pairing.parsePairKey(entry);\n      if (!parsed) {\n        removed.push(entry);\n        continue;\n      }\n\n      const candidates = actualPairsByType[parsed.type];\n      const matched = 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parsePairKey(value: string): ParsedPairKey | null {\n    const parts = value.split(\"|\");\n    if (parts.length !== 3) {\n      log(\"Invalid pair key format: %s\", value);\n      return null;\n    }\n    const [typeRaw, leftRaw, rightRaw] = parts;\n    const type = this.stringToUnitType(typeRaw);\n    if (!type) {\n      log(\"Unknown unit type in pair key: %s\", typeRaw);\n      return null;\n    }\n    const [left, right] = [leftRaw, rightRaw].sort();\n    return { type, left, right, key: `${type}|${left}|${right}` };\n  }\n\n  /**\n   * Checks whether an actual pair key satisfies a pattern, with glob matching for class paths.\n   */\n  pairKeyMatches(actual: ParsedPairKey, pattern: ParsedPairKey): boolean {\n    if (actual.type !== pattern.type) return false;\n    if (actual.type === IndexUnitType.CLASS) {\n      // Allow glob matching for class file paths.\n      const forward =\n        minimatch(actual.left, pattern.left, { dot: true }) &&\n        minimatch(actual.right, pattern.right, { dot: true });\n      const swapped =\n        minimatch(actual.left, pattern.right, { dot: true }) &&\n        minimatch(actual.right, pattern.left, { dot: true });\n      return forward || swapped;\n    }\n\n    // Functions and blocks use exact matching on canonical strings.\n    return (\n      (actual.left === pattern.left && actual.right === pattern.right) ||\n      (actual.left === pattern.right && actual.right === pattern.left)\n    );\n  }\n\n  /**\n   * Derives a reversible, extractor-aware label for a unit.\n   * Extractors may override; fallback uses a fixed format per unit type.\n   */\n  unitLabel(unit: UnitLike): string {\n    const extractor = this.findExtractor(unit.filePath);\n    const customLabel = extractor?.unitLabel?.(unit as IndexUnit);\n    if (customLabel) return customLabel;\n\n    switch (unit.unitType) {\n      case IndexUnitType.CLASS:\n        return unit.filePath;\n      case IndexUnitType.FUNCTION:\n        return 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+{"version":3,"sources":["../src/DryScan.ts","../src/const.ts","../src/IndexUnitExtractor.ts","../src/extractors/java.ts","../src/config/indexConfig.ts","../src/config/configStore.ts","../src/config/dryconfig.ts","../src/Gitignore.ts","../src/db/DryScanDatabase.ts","../src/db/entities/FileEntity.ts","../src/db/entities/IndexUnitEntity.ts","../src/services/RepositoryInitializer.ts","../src/services/EmbeddingService.ts","../src/services/UpdateService.ts","../src/DryScanUpdater.ts","../src/services/DuplicationCache.ts","../src/services/DuplicateService.ts","../src/services/ExclusionService.ts","../src/services/PairingService.ts"],"sourcesContent":["import upath from \"upath\";\nimport fs from \"fs/promises\";\nimport { DuplicateAnalysisResult, DuplicateReport } from \"./types\";\nimport { DRYSCAN_DIR, INDEX_DB } from \"./const\";\nimport { defaultExtractors, IndexUnitExtractor } from \"./IndexUnitExtractor\";\nimport { DryScanDatabase } from \"./db/DryScanDatabase\";\nimport { RepositoryInitializer, InitOptions as InitServiceOptions } from \"./services/RepositoryInitializer\";\nimport { UpdateService } from \"./services/UpdateService\";\nimport { DuplicateService } from \"./services/DuplicateService\";\nimport { ExclusionService } from \"./services/ExclusionService\";\nimport { DryScanServiceDeps } from \"./services/types\";\nimport { configStore } from \"./config/configStore\";\nimport { DryConfig } from \"./types\";\nimport { PairingService } from \"./services/PairingService\";\nimport { existsSync } from \"fs\";\n\nexport type InitOptions = InitServiceOptions;\n\n\nexport class DryScan {\n  repoPath: string;\n  private readonly extractor: IndexUnitExtractor;\n  private db: DryScanDatabase;\n  private readonly services: {\n    initializer: RepositoryInitializer;\n    updater: UpdateService;\n    duplicate: DuplicateService;\n    exclusion: ExclusionService;\n  };\n  private readonly serviceDeps: DryScanServiceDeps;\n\n  constructor(\n    repoPath: string,\n    extractor?: IndexUnitExtractor,\n    db?: DryScanDatabase\n  ) {\n    this.repoPath = repoPath;\n    this.extractor = extractor ?? new IndexUnitExtractor(repoPath, defaultExtractors(repoPath));\n    this.db = db ?? new DryScanDatabase();\n\n    this.serviceDeps = {\n      repoPath: this.repoPath,\n      db: this.db,\n      extractor: this.extractor,\n      pairing: new PairingService(this.extractor),\n    };\n\n    const exclusion = new ExclusionService(this.serviceDeps);\n    this.services = {\n      initializer: new RepositoryInitializer(this.serviceDeps, exclusion),\n      updater: new UpdateService(this.serviceDeps, exclusion),\n      duplicate: new DuplicateService(this.serviceDeps),\n      exclusion,\n    };\n  }\n\n  /**\n   * Initializes the DryScan repository with a 3-phase analysis:\n   * Phase 1: Extract and save all functions\n   * Phase 2: Resolve and save internal dependencies\n   * Phase 3: Compute and save semantic embeddings\n   */\n  async init(options?: InitOptions): Promise<void> {\n    console.log(`[DryScan] Initializing repository at ${this.repoPath}`);\n\n    const dryDir = upath.join(this.repoPath, DRYSCAN_DIR);\n    if (existsSync(dryDir)) {\n      console.warn(`[DryScan] Warning: a '.dry' folder already exists at ${dryDir}.`);\n    }\n    console.log(\"[DryScan] Preparing database and cache...\");\n    await configStore.init(this.repoPath);\n    await this.ensureDatabase();\n    console.log(\"[DryScan] Starting initial scan (may take a moment)...\");\n    await this.services.initializer.init(options);\n    console.log(\"[DryScan] Initial scan complete.\");\n  }\n\n  /**\n   * Updates the index by detecting changed, new, and deleted files.\n   * Only reprocesses units in changed files for efficiency.\n   * Delegates to DryScanUpdater module for implementation.\n   * \n   * Update process:\n   * 1. 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Honors exclusion globs from config.\n   */\n  async listSourceFiles(dirPath: string): Promise<string[]> {\n    const target = await this.resolveTarget(dirPath);\n    const config = await this.loadConfig();\n    const ignoreMatcher = await this.gitignore.buildMatcher(config);\n\n    if (target.stat.isFile()) {\n      return this.filterSingleFile(target.baseRel, ignoreMatcher);\n    }\n\n    const matches = await this.globSourceFiles(target.baseRel);\n    return this.filterSupportedFiles(matches, ignoreMatcher);\n  }\n\n  /**\n   * Computes MD5 checksum of file content to track changes.\n   */\n  async computeChecksum(filePath: string): Promise<string> {\n    const fullPath = path.isAbsolute(filePath)\n      ? filePath\n      : path.join(this.root, filePath);\n\n    const content = await fs.readFile(fullPath, \"utf8\");\n    return crypto.createHash(FILE_CHECKSUM_ALGO).update(content).digest(\"hex\");\n  }\n\n  /**\n   * Scans a file or directory and extracts indexable units using the matching LanguageExtractor.\n   * The returned units have repo-relative file paths and no embedding attached.\n   */\n  async scan(targetPath: string): Promise<IndexUnit[]> {\n    const fullPath = path.isAbsolute(targetPath)\n      ? targetPath\n      : path.join(this.root, targetPath);\n\n    const stat = await fs.stat(fullPath).catch(() => null);\n    if (!stat) {\n      throw new Error(`Path not found: ${fullPath}`);\n    }\n\n    if (stat.isDirectory()) {\n      log(\"Scanning directory %s\", fullPath);\n      return this.scanDirectory(fullPath);\n    }\n\n    return this.scanFile(fullPath);\n  }\n\n\n  /**\n   * Scans a directory recursively, extracting units from supported files while honoring exclusions.\n   */\n  private async scanDirectory(dir: string): Promise<IndexUnit[]> {\n    const out: IndexUnit[] = [];\n    const relDir = this.relPath(dir);\n    const files = await this.listSourceFiles(relDir);\n    for (const relFile of files) {\n      const absFile = path.join(this.root, relFile);\n      const extracted = await this.tryScanSupportedFile(absFile);\n      out.push(...extracted);\n    }\n    return out;\n  }\n\n  /**\n   * Scans a single file and extracts supported units.\n   */\n  private async scanFile(filePath: string): Promise<IndexUnit[]> {\n    return this.tryScanSupportedFile(filePath, true);\n  }\n\n  /**\n   * Extracts units from a supported file.\n   * Optionally throws when the file type is unsupported (used when scanning an explicit file).\n   */\n  private async tryScanSupportedFile(filePath: string, throwOnUnsupported = false): Promise<IndexUnit[]> {\n    const extractor = this.extractors.find(ex => ex.supports(filePath));\n    if (!extractor) {\n      if (throwOnUnsupported) {\n        throw new Error(`Unsupported file type: ${filePath}`);\n      }\n      return [];\n    }\n    const rel = this.relPath(filePath);\n    if (await this.shouldExclude(rel)) {\n      log(\"Skipping excluded file %s\", rel);\n      return [];\n    }\n    const source = await fs.readFile(filePath, \"utf8\");\n    const units = await extractor.extractFromText(rel, source);\n    log(\"Extracted %d units from %s\", units.length, rel);\n    return units.map(unit => ({\n      ...unit,\n      filePath: rel,\n      embedding: undefined,\n    }));\n  }\n\n  /**\n   * Converts an absolute path to a repo-relative, normalized (POSIX-style) path.\n   * This keeps paths stable across platforms and consistent in the index/DB.\n   */\n  private relPath(absPath: string): string {\n    return this.normalizeRelPath(upath.relative(this.root, absPath));\n  }\n\n  /**\n   * Returns true if a repo-relative path matches any configured exclusion glob.\n   */\n  private async shouldExclude(relPath: string): Promise<boolean> {\n    const config = await this.loadConfig();\n    const ignoreMatcher = await this.gitignore.buildMatcher(config);\n    return ignoreMatcher.ignores(this.normalizeRelPath(relPath));\n  }\n\n  private async loadConfig(): Promise<DryConfig> {\n    return await configStore.get(this.root);\n  }\n\n  /**\n   * Normalizes repo-relative paths and strips leading \"./\" to keep matcher inputs consistent.\n   */\n  private normalizeRelPath(relPath: string): string {\n    const normalized = upath.normalizeTrim(relPath);\n    return normalized.startsWith(\"./\") ? normalized.slice(2) : normalized;\n  }\n\n  private async resolveTarget(dirPath: string): Promise<{ fullPath: string; baseRel: string; stat: Stats; }> {\n    const fullPath = path.isAbsolute(dirPath) ? dirPath : path.join(this.root, dirPath);\n    const stat = await fs.stat(fullPath).catch(() => null);\n    if (!stat) {\n      throw new Error(`Path not found: ${fullPath}`);\n    }\n    const baseRel = this.relPath(fullPath);\n    log(\"Listing source files under %s\", fullPath);\n    return { fullPath, baseRel, stat };\n  }\n\n  private async filterSingleFile(baseRel: string, ignoreMatcher: Ignore): Promise<string[]> {\n    const relFile = this.normalizeRelPath(baseRel);\n    if (ignoreMatcher.ignores(relFile)) return [];\n    return this.extractors.some((ex) => ex.supports(relFile)) ? [relFile] : [];\n  }\n\n  private async globSourceFiles(baseRel: string): Promise<string[]> {\n    const pattern = baseRel ? `${baseRel.replace(/\\\\/g, \"/\")}/**/*` : \"**/*\";\n    const matches = await glob(pattern, {\n      cwd: this.root,\n      dot: false,\n      nodir: true,\n    });\n    return matches.map((p: string) => this.normalizeRelPath(p));\n  }\n\n  private filterSupportedFiles(relPaths: string[], ignoreMatcher: Ignore): string[] {\n    return relPaths\n      .filter((relPath: string) => !ignoreMatcher.ignores(relPath))\n      .filter((relPath: string) => this.extractors.some((ex) => ex.supports(relPath)));\n  }\n}\n","import crypto from \"node:crypto\";\nimport Parser from \"tree-sitter\";\nimport Java from \"tree-sitter-java\";\nimport { LanguageExtractor } from \"./LanguageExtractor\";\nimport { IndexUnit, IndexUnitType } from \"../types\";\nimport { indexConfig } from \"../config/indexConfig\";\nimport { DryConfig } from \"../types\";\nimport { configStore } from \"../config/configStore\";\nimport { BLOCK_HASH_ALGO } from \"../const\";\n\nexport class JavaExtractor implements LanguageExtractor {\n  readonly id = \"java\";\n  readonly exts = [\".java\"];\n\n  private parser: Parser;\n  private readonly repoPath: string;\n  private config?: DryConfig;\n\n  constructor(repoPath: string) {\n    this.repoPath = repoPath;\n    this.parser = new Parser();\n    this.parser.setLanguage(Java);\n  }\n\n  supports(filePath: string): boolean {\n    const lower = filePath.toLowerCase();\n    return this.exts.some((ext) => lower.endsWith(ext));\n  }\n\n  async extractFromText(fileRelPath: string, source: string): Promise<IndexUnit[]> {\n    if (!source.trim()) return [];\n\n    this.config = await configStore.get(this.repoPath);\n\n    const tree = this.parser.parse(source);\n    const units: IndexUnit[] = [];\n\n    const visit = (node: Parser.SyntaxNode, currentClass?: IndexUnit) => {\n      if (this.isClassNode(node)) {\n        const className = this.getClassName(node, source) || \"<anonymous>\";\n        if (this.isDtoClass(node, source, className)) {\n          return;\n        }\n        const startLine = node.startPosition.row;\n        const endLine = node.endPosition.row;\n        const classLength = endLine - startLine;\n        const skipClass = this.shouldSkip(IndexUnitType.CLASS, className, classLength);\n        const classId = this.buildId(IndexUnitType.CLASS, className, startLine, endLine);\n        const code = this.stripComments(this.stripClassBody(node, source));\n        const classUnit: IndexUnit = {\n          id: classId,\n          name: className,\n          filePath: fileRelPath,\n          startLine,\n          endLine,\n          code,\n          unitType: IndexUnitType.CLASS,\n          children: [],\n        };\n        if (!skipClass) {\n          units.push(classUnit);\n        }\n\n        for (let i = 0; i < node.namedChildCount; i++) {\n          const child = node.namedChild(i);\n          if (child) visit(child, skipClass ? undefined : classUnit);\n        }\n        return;\n      }\n\n      if (this.isFunctionNode(node)) {\n        const fnUnit = this.buildFunctionUnit(node, source, fileRelPath, currentClass);\n        const fnLength = fnUnit.endLine - fnUnit.startLine;\n        const bodyNode = this.getFunctionBody(node);\n        const skipFunction = this.shouldSkip(IndexUnitType.FUNCTION, fnUnit.name, fnLength);\n\n        if (skipFunction) {\n          return;\n        }\n\n        units.push(fnUnit);\n\n        if (bodyNode) {\n          const blocks = this.extractBlocks(bodyNode, source, fileRelPath, fnUnit);\n          units.push(...blocks);\n        }\n      }\n\n      for (let i = 0; i < node.namedChildCount; i++) {\n        const child = node.namedChild(i);\n        if (child) visit(child, currentClass);\n      }\n    };\n\n    visit(tree.rootNode);\n\n    //remove duplicates if any\n    return this.removeDuplicates(units);\n  }\n\n  unitLabel(unit: IndexUnit): string | null {\n    if (unit.unitType === IndexUnitType.CLASS) return unit.filePath;\n    if (unit.unitType === IndexUnitType.FUNCTION) return this.canonicalFunctionSignature(unit);\n    if (unit.unitType === IndexUnitType.BLOCK) return this.normalizedBlockHash(unit);\n    return unit.name;\n  }\n\n  private isClassNode(node: Parser.SyntaxNode): boolean {\n    return node.type === \"class_declaration\";\n  }\n\n  private getClassName(node: Parser.SyntaxNode, source: string): string | null {\n    const nameNode = node.childForFieldName?.(\"name\");\n    return nameNode ? source.slice(nameNode.startIndex, nameNode.endIndex) : null;\n  }\n\n  private isFunctionNode(node: Parser.SyntaxNode): boolean {\n    return node.type === \"method_declaration\" || node.type === \"constructor_declaration\";\n  }\n\n  private getFunctionName(node: Parser.SyntaxNode, source: string, parentClass?: IndexUnit): string | null {\n    const nameNode = node.childForFieldName?.(\"name\");\n    const nameText = nameNode ? source.slice(nameNode.startIndex, nameNode.endIndex) : \"<anonymous>\";\n    return parentClass ? `${parentClass.name}.${nameText}` : nameText;\n  }\n\n  private getFunctionBody(node: Parser.SyntaxNode): Parser.SyntaxNode | null {\n    return node.childForFieldName?.(\"body\") ?? null;\n  }\n\n  private isBlockNode(node: Parser.SyntaxNode): boolean {\n    return node.type === \"block\";\n  }\n\n  private getMethodBodiesForClass(node: Parser.SyntaxNode): Parser.SyntaxNode[] {\n    const bodies: Parser.SyntaxNode[] = [];\n    const classBody = node.children.find(child => child.type === \"class_body\");\n    if (!classBody) return bodies;\n    \n    for (let i = 0; i < classBody.namedChildCount; i++) {\n      const child = classBody.namedChild(i);\n      if (!child) continue;\n      if (child.type === \"method_declaration\" || child.type === \"constructor_declaration\") {\n        const body = child.childForFieldName?.(\"body\");\n        if (body) bodies.push(body);\n      }\n    }\n    return bodies;\n  }\n\n  private canonicalFunctionSignature(unit: IndexUnit): string {\n    const arity = this.extractArity(unit.code);\n    return `${unit.name}(arity:${arity})`;\n  }\n\n  private normalizedBlockHash(unit: IndexUnit): string {\n    const normalized = this.normalizeCode(unit.code);\n    return crypto.createHash(BLOCK_HASH_ALGO).update(normalized).digest(\"hex\");\n  }\n\n  private shouldSkip(unitType: IndexUnitType, name: string, lineCount: number): boolean {\n    if (!this.config) {\n      throw new Error(\"Config not loaded before skip evaluation\");\n    }\n    const config = this.config;\n    const minLines = unitType === IndexUnitType.BLOCK\n      ? Math.max(indexConfig.blockMinLines, config.minBlockLines ?? 0)\n      : config.minLines;\n    const belowMin = minLines > 0 && lineCount < minLines;\n    const trivial = unitType === IndexUnitType.FUNCTION && this.isTrivialFunction(name);\n    return belowMin || trivial;\n  }\n\n  private isTrivialFunction(fullName: string): boolean {\n    const simpleName = fullName.split(\".\").pop() || fullName;\n    const isGetter = /^(get|is)[A-Z]/.test(simpleName);\n    const isSetter = /^set[A-Z]/.test(simpleName);\n    return isGetter || isSetter;\n  }\n\n  private isDtoClass(node: Parser.SyntaxNode, source: string, className: string): boolean {\n    const classBody = node.children.find((child) => child.type === \"class_body\");\n    if (!classBody) return false;\n\n    let hasField = false;\n\n    for (let i = 0; i < classBody.namedChildCount; i++) {\n      const child = classBody.namedChild(i);\n      if (!child) continue;\n\n      if (child.type === \"field_declaration\") {\n        hasField = true;\n        continue;\n      }\n\n      if (child.type.includes(\"annotation\")) {\n        continue;\n      }\n\n      if (child.type === \"method_declaration\" || child.type === \"constructor_declaration\") {\n        const simpleName = this.getSimpleFunctionName(child, source);\n        const fullName = `${className}.${simpleName}`;\n        if (!this.isTrivialFunction(fullName)) {\n          return false;\n        }\n        continue;\n      }\n\n      return false;\n    }\n\n    return hasField;\n  }\n\n  private getSimpleFunctionName(node: Parser.SyntaxNode, source: string): string {\n    const nameNode = node.childForFieldName?.(\"name\");\n    return nameNode ? source.slice(nameNode.startIndex, nameNode.endIndex) : \"<anonymous>\";\n  }\n\n  private buildFunctionUnit(\n    node: Parser.SyntaxNode,\n    source: string,\n    file: string,\n    parentClass?: IndexUnit\n  ): IndexUnit {\n    const name = this.getFunctionName(node, source, parentClass) || \"<anonymous>\";\n    const startLine = node.startPosition.row;\n    const endLine = node.endPosition.row;\n    const id = this.buildId(IndexUnitType.FUNCTION, name, startLine, endLine);\n    const unit: IndexUnit = {\n      id,\n      name,\n      filePath: file,\n      startLine,\n      endLine,\n      children: [],\n      code: this.stripComments(source.slice(node.startIndex, node.endIndex)),\n      unitType: IndexUnitType.FUNCTION,\n      parentId: parentClass?.id,\n      parent: parentClass,\n    };\n    if (parentClass) {\n      parentClass.children = parentClass.children || [];\n      parentClass.children.push(unit);\n    }\n    return unit;\n  }\n\n  private extractBlocks(\n    bodyNode: Parser.SyntaxNode,\n    source: string,\n    file: string,\n    parentFunction: IndexUnit\n  ): IndexUnit[] {\n    const blocks: IndexUnit[] = [];\n\n    const visit = (n: Parser.SyntaxNode) => {\n      if (this.isBlockNode(n)) {\n        const startLine = n.startPosition.row;\n        const endLine = n.endPosition.row;\n        const lineCount = endLine - startLine;\n        if (this.shouldSkip(IndexUnitType.BLOCK, parentFunction.name, lineCount)) {\n          return;\n        }\n        if (lineCount >= indexConfig.blockMinLines) {\n          const id = this.buildId(IndexUnitType.BLOCK, parentFunction.name, startLine, endLine);\n          const blockUnit: IndexUnit = {\n            id,\n            name: parentFunction.name,\n            filePath: file,\n            startLine,\n            endLine,\n            code: this.stripComments(source.slice(n.startIndex, n.endIndex)),\n            unitType: IndexUnitType.BLOCK,\n            parentId: parentFunction.id,\n            parent: parentFunction,\n          };\n          const contextLength = this.config?.contextLength ?? 2048;\n          const splitBlocks = this.textSplitBlockIfOverContextLimit(blockUnit, contextLength);\n          parentFunction.children = parentFunction.children || [];\n          parentFunction.children.push(...splitBlocks);\n          blocks.push(...splitBlocks);\n        }\n      }\n\n      for (let i = 0; i < n.namedChildCount; i++) {\n        const child = n.namedChild(i);\n        if (child) visit(child);\n      }\n    };\n\n    visit(bodyNode);\n    return blocks;\n  }\n\n  private stripClassBody(node: Parser.SyntaxNode, source: string): string {\n    const classStart = node.startIndex;\n    let code = source.slice(classStart, node.endIndex);\n\n    const methodBodies: Array<{ start: number; end: number }> = [];\n    const candidates = this.getMethodBodiesForClass(node);\n\n    for (const body of candidates) {\n      methodBodies.push({ start: body.startIndex - classStart, end: body.endIndex - classStart });\n    }\n\n    methodBodies.sort((a, b) => b.start - a.start);\n    for (const body of methodBodies) {\n      code = code.slice(0, body.start) + \" { }\" + code.slice(body.end);\n    }\n\n    return code;\n  }\n\n  private buildId(type: IndexUnitType, name: string, startLine: number, endLine: number): string {\n    return `${type}:${name}:${startLine}-${endLine}`;\n  }\n\n  private extractArity(code: string): number {\n    const match = code.match(/^[^{]*?\\(([^)]*)\\)/s);\n    if (!match) return 0;\n    const params = match[1]\n      .split(\",\")\n      .map((p) => p.trim())\n      .filter(Boolean);\n    return params.length;\n  }\n\n  private normalizeCode(code: string): string {\n    const withoutBlockComments = code.replace(/\\/\\*[\\s\\S]*?\\*\\//g, \"\");\n    const withoutLineComments = withoutBlockComments.replace(/\\/\\/[^\\n\\r]*/g, \"\");\n    return withoutLineComments.replace(/\\s+/g, \"\");\n  }\n\n  private stripComments(code: string): string {\n    const withoutBlockComments = code.replace(/\\/\\*[\\s\\S]*?\\*\\//g, (match) => match.replace(/[^\\n\\r]/g, \"\"));\n    return withoutBlockComments.replace(/\\/\\/[^\\n\\r]*/g, \"\");\n  }\n\n  private removeDuplicates(units: IndexUnit[]): IndexUnit[] | PromiseLike<IndexUnit[]> {\n    return Array.from(new Map(units.map(u => [u.id, u])).values());\n  }\n\n  /** Splits a block unit's code into chunks if it exceeds the context length limit. */\n  private textSplitBlockIfOverContextLimit(unit: IndexUnit, contextLength: number): IndexUnit[] {\n    if (unit.code.length <= contextLength) return [unit];\n\n    const chunks: IndexUnit[] = [];\n    let chunkIndex = 0;\n    for (let i = 0; i < unit.code.length; i += contextLength) {\n      chunks.push({\n        ...unit,\n        id: `${unit.id}:chunk${chunkIndex}`,\n        code: unit.code.slice(i, i + contextLength),\n      });\n      chunkIndex++;\n    }\n    return chunks;\n  }\n}\n\n","export const indexConfig = {\n  blockMinLines: 5,\n  thresholds: {\n    class: 0.88,\n    function: 0.88,\n    block: 0.88,\n  },\n  weights: {\n    class: { self: 1 },\n    function: { self: 0.8, parentClass: 0.2 },\n    block: { self: 0.7, parentFunction: 0.2, parentClass: 0.1 },\n  },\n};\n","import upath from \"upath\";\nimport { DryConfig } from \"../types\";\nimport { ensureDefaultConfig, resolveDryConfig, saveDryConfig } from \"./dryconfig\";\n\nclass ConfigStore {\n  private readonly cache = new Map<string, DryConfig>();\n  private readonly loading = new Map<string, Promise<DryConfig>>();\n\n  async init(repoPath: string): Promise<DryConfig> {\n    const key = this.normalize(repoPath);\n    return this.load(key, repoPath);\n  }\n\n  async get(repoPath: string): Promise<DryConfig> {\n    const key = this.normalize(repoPath);\n    const cached = this.cache.get(key);\n    if (cached) return cached;\n    return this.load(key, repoPath);\n  }\n\n  async refresh(repoPath: string): Promise<DryConfig> {\n    const key = this.normalize(repoPath);\n    this.cache.delete(key);\n    return this.load(key, repoPath);\n  }\n\n  async save(repoPath: string, config: DryConfig): Promise<void> {\n    const key = this.normalize(repoPath);\n    await saveDryConfig(repoPath, config);\n    this.cache.set(key, config);\n  }\n\n  private async load(key: string, repoPath: string): Promise<DryConfig> {\n    const existing = this.loading.get(key);\n    if (existing) return existing;\n\n    const promise = ensureDefaultConfig(repoPath).then(() => resolveDryConfig(repoPath)).then((config) => {\n      this.cache.set(key, config);\n      this.loading.delete(key);\n      return config;\n    }).catch((err) => {\n      this.loading.delete(key);\n      throw err;\n    });\n\n    this.loading.set(key, promise);\n    return promise;\n  }\n\n  private normalize(repoPath: string): string {\n    return upath.normalizeTrim(upath.resolve(repoPath));\n  }\n}\n\nexport const configStore = new ConfigStore();\n","import fs from \"fs/promises\";\nimport upath from \"upath\";\nimport { Validator, Schema } from \"jsonschema\";\nimport { DryConfig } from \"../types\";\n\n// Baseline config used when no file is present; exported so tests and constructors can seed defaults.\nexport const DEFAULT_CONFIG: DryConfig = {\n  excludedPaths: [\n    \"**/test/**\",\n  ],\n  excludedPairs: [],\n  minLines: 3,\n  minBlockLines: 5,\n  threshold: 0.88,\n  embeddingSource: \"http://localhost:11434\",\n  contextLength: 2048,\n};\n\nconst validator = new Validator();\n\nconst partialConfigSchema: Schema = {\n  type: \"object\",\n  properties: {\n    excludedPaths: { type: \"array\", items: { type: \"string\" } },\n    excludedPairs: { type: \"array\", items: { type: \"string\" } },\n    minLines: { type: \"number\" },\n    minBlockLines: { type: \"number\" },\n    threshold: { type: \"number\" },\n    embeddingSource: { type: \"string\" },\n    contextLength: { type: \"number\" },\n  },\n};\n\nconst fullConfigSchema: Schema = {\n  ...partialConfigSchema,\n  required: [\n    \"excludedPaths\",\n    \"excludedPairs\",\n    \"minLines\",\n    \"minBlockLines\",\n    \"threshold\",\n    \"embeddingSource\",\n    \"contextLength\",\n  ],\n};\n\nfunction validateConfig(raw: unknown, schema: Schema, source: string): any {\n  const result = validator.validate(raw, schema);\n  if (!result.valid) {\n    const details = result.errors.map((e) => e.stack).join(\"; \");\n    throw new Error(`${source} config is invalid: ${details}`);\n  }\n  return raw;\n}\n\nasync function readConfigFile(repoPath: string): Promise<Partial<DryConfig>> {\n  const configPath = upath.join(repoPath, \"dryconfig.json\");\n  try {\n    const content = await fs.readFile(configPath, \"utf8\");\n    let parsed: Partial<DryConfig> = {};\n    try {\n      parsed = JSON.parse(content) as Partial<DryConfig>;\n    } catch (parseErr) {\n      throw new Error(`Invalid JSON in ${configPath}: ${(parseErr as Error).message}`);\n    }\n    return parsed;\n  } catch (err: any) {\n    if (err?.code === \"ENOENT\") {\n      return {};\n    }\n    throw err;\n  }\n}\n\n/**\n * Resolves the effective config for a repo using defaults merged with any file config.\n */\nexport async function resolveDryConfig(repoPath: string): Promise<DryConfig> {\n  const fileConfigRaw = await readConfigFile(repoPath);\n  validateConfig(fileConfigRaw, partialConfigSchema, \"Config file\");\n\n  const merged = { ...DEFAULT_CONFIG, ...fileConfigRaw };\n  validateConfig(merged, fullConfigSchema, \"Merged\");\n  return merged as DryConfig;\n}\n\n// Backwards-compatible helper used by existing callers (file + defaults).\nexport async function loadDryConfig(repoPath: string): Promise<DryConfig> {\n  return resolveDryConfig(repoPath);\n}\n\nexport async function saveDryConfig(repoPath: string, config: DryConfig): Promise<void> {\n  const configPath = upath.join(repoPath, \"dryconfig.json\");\n  validateConfig(config, fullConfigSchema, \"Config to save\");\n  await fs.writeFile(configPath, JSON.stringify(config, null, 2), \"utf8\");\n}\n\nexport async function ensureDefaultConfig(repoPath: string): Promise<void> {\n  const configPath = upath.join(repoPath, \"dryconfig.json\");\n  const repoExists = await fs.stat(repoPath).then((s) => s.isDirectory()).catch((err: any) => {\n    if (err?.code === \"ENOENT\") return false;\n    throw err;\n  });\n\n  if (!repoExists) return;\n\n  const exists = await fs.stat(configPath).then(() => true).catch((err: any) => {\n    if (err?.code === \"ENOENT\") return false;\n    throw err;\n  });\n\n  if (!exists) {\n    await saveDryConfig(repoPath, DEFAULT_CONFIG);\n  }\n}\n","import path from \"path\";\nimport fs from \"fs/promises\";\nimport upath from \"upath\";\nimport { glob } from \"glob-gitignore\";\nimport ignore, { Ignore } from \"ignore\";\nimport { DryConfig } from \"./types\";\n\n/**\n * Gitignore helper that builds ignore matchers by combining default rules,\n * repo .gitignore files, and config-driven exclusions.\n */\nexport class Gitignore {\n  private readonly defaultIgnores = [\".git/**\", \".dry/**\"];\n\n  constructor(private readonly root: string) {}\n\n  async buildMatcher(config: DryConfig): Promise<Ignore> {\n    const rules = await this.resolveRules(config);\n    return ignore({ allowRelativePaths: true }).add(rules);\n  }\n\n  private async resolveRules(config: DryConfig): Promise<string[]> {\n    const gitignoreRules = await this.loadGitignoreRules();\n    const configRules = config.excludedPaths || [];\n    return [...this.defaultIgnores, ...gitignoreRules, ...configRules];\n  }\n\n  private async loadGitignoreRules(): Promise<string[]> {\n    const gitignoreFiles = await glob(\"**/.gitignore\", {\n      cwd: this.root,\n      dot: true,\n      nodir: true,\n      ignore: this.defaultIgnores,\n    });\n\n    const rules: string[] = [];\n\n    for (const file of gitignoreFiles) {\n      const absPath = path.join(this.root, file);\n      const dir = upath.normalizeTrim(upath.dirname(file));\n      const content = await fs.readFile(absPath, \"utf8\").catch(() => \"\");\n      const lines = content.split(/\\r?\\n/);\n\n      for (const raw of lines) {\n        const trimmed = raw.trim();\n        if (!trimmed || trimmed.startsWith(\"#\")) continue;\n\n        const negated = trimmed.startsWith(\"!\");\n        const body = negated ? trimmed.slice(1) : trimmed;\n\n        const scoped = this.scopeRule(body, dir);\n        if (!scoped) continue;\n\n        rules.push(negated ? `!${scoped}` : scoped);\n      }\n    }\n\n    return rules;\n  }\n\n  private scopeRule(rule: string, gitignoreDir: string): string | null {\n    const cleaned = rule.replace(/^\\//, \"\");\n    if (!cleaned) return null;\n\n    if (!gitignoreDir || gitignoreDir === \".\") {\n      return cleaned;\n    }\n\n    return upath.normalizeTrim(upath.join(gitignoreDir, cleaned));\n  }\n}\n","import \"reflect-metadata\";\nimport fs from \"fs/promises\";\nimport upath from \"upath\";\nimport { DataSource, Repository, In } from \"typeorm\";\nimport { FileEntity } from \"./entities/FileEntity\";\nimport { IndexUnit } from \"../types\";\nimport { IndexUnitEntity } from \"./entities/IndexUnitEntity\";\n\nexport class DryScanDatabase {\n  private dataSource?: DataSource;\n  private unitRepository?: Repository<IndexUnitEntity>;\n  private fileRepository?: Repository<FileEntity>;\n\n  isInitialized(): boolean {\n    return !!this.dataSource?.isInitialized;\n  }\n\n  async init(dbPath: string): Promise<void> {\n    await fs.mkdir(upath.dirname(dbPath), { recursive: true });\n\n    this.dataSource = new DataSource({\n      type: \"sqlite\",\n      database: dbPath,\n      entities: [IndexUnitEntity, FileEntity],\n      synchronize: true,\n      logging: false,\n    });\n\n    await this.dataSource.initialize();\n    this.unitRepository = this.dataSource.getRepository(IndexUnitEntity);\n    this.fileRepository = this.dataSource.getRepository(FileEntity);\n  }\n\n  async saveUnit(unit: IndexUnit): Promise<void> {\n    await this.saveUnits(unit);\n  }\n\n  async saveUnits(units: IndexUnit | IndexUnit[]): Promise<void> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    const payload = Array.isArray(units) ? units : [units];\n    const BATCH_SIZE = 500;\n    for (let i = 0; i < payload.length; i += BATCH_SIZE) {\n      console.debug(`[DryScanDatabase] Saving units ${i + 1}-${Math.min(i + BATCH_SIZE, payload.length)} of ${payload.length}...`);\n      const batch = payload.slice(i, i + BATCH_SIZE);\n      await this.unitRepository.save(batch);\n    }\n  }\n\n  async getUnit(id: string): Promise<IndexUnit | null> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    return this.unitRepository.findOne({\n      where: { id },\n      relations: [\"children\", \"parent\"]\n    });\n  }\n\n  async getAllUnits(): Promise<IndexUnit[]> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    return this.unitRepository.find({ relations: [\"children\", \"parent\"] });\n  }\n\n  async updateUnit(unit: IndexUnit): Promise<void> {\n    await this.saveUnits(unit);\n  }\n\n  async updateUnits(units: IndexUnit | IndexUnit[]): Promise<void> {\n    await this.saveUnits(units);\n  }\n\n  /**\n   * Returns total count of indexed units.\n   */\n  async countUnits(): Promise<number> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    return this.unitRepository.count();\n  }\n\n  /**\n   * Removes index units by their file paths.\n   * Used during incremental updates when files change.\n   */\n  async removeUnitsByFilePaths(filePaths: string[]): Promise<void> {\n    if (!this.unitRepository) throw new Error(\"Database not initialized\");\n    await this.unitRepository.delete({ filePath: In(filePaths) });\n  }\n\n  /**\n   * Saves file metadata (path, checksum, mtime) to track changes.\n   */\n  async saveFile(file: FileEntity): Promise<void> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    await this.fileRepository.save(file);\n  }\n\n  /**\n   * Saves multiple file metadata entries.\n   */\n  async saveFiles(files: FileEntity[]): Promise<void> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    await this.fileRepository.save(files);\n  }\n\n  /**\n   * Gets file metadata by file path.\n   */\n  async getFile(filePath: string): Promise<FileEntity | null> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    return this.fileRepository.findOne({ where: { filePath } });\n  }\n\n  /**\n   * Gets all tracked files.\n   */\n  async getAllFiles(): Promise<FileEntity[]> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    return this.fileRepository.find();\n  }\n\n  /**\n   * Removes file metadata entries by file paths.\n   * Used when files are deleted from repository.\n   */\n  async removeFilesByFilePaths(filePaths: string[]): Promise<void> {\n    if (!this.fileRepository) throw new Error(\"Database not initialized\");\n    await this.fileRepository.delete({ filePath: In(filePaths) });\n  }\n\n  async close(): Promise<void> {\n    if (this.dataSource?.isInitialized) {\n      await this.dataSource.destroy();\n    }\n  }\n}\n","import { Entity, PrimaryColumn, Column } from \"typeorm\";\n\n/**\n * Represents a tracked source file in the repository.\n * Used to detect changes via checksum and mtime for incremental updates.\n */\n@Entity(\"files\")\nexport class FileEntity {\n  /**\n   * Relative path to the file from repository root.\n   * Used as primary key for uniqueness.\n   */\n  @PrimaryColumn(\"text\")\n  filePath!: string;\n\n  /**\n   * MD5 checksum of file content.\n   * Used to detect content changes.\n   */\n  @Column(\"text\")\n  checksum!: string;\n\n  /**\n   * Last modification time in milliseconds since epoch.\n   * Used as fast sanity check before computing checksum.\n   */\n  @Column(\"integer\")\n  mtime!: number;\n}\n","import {\n  Column,\n  Entity,\n  JoinColumn,\n  ManyToOne,\n  OneToMany,\n  PrimaryColumn,\n  RelationId,\n} from \"typeorm\";\nimport { IndexUnit, IndexUnitType } from \"../../types\";\n\n@Entity(\"index_units\")\nexport class IndexUnitEntity implements IndexUnit {\n  @PrimaryColumn(\"text\")\n  id!: string;\n\n  @Column(\"text\")\n  name!: string;\n\n  @Column(\"text\")\n  filePath!: string;\n\n  @Column(\"integer\")\n  startLine!: number;\n\n  @Column(\"integer\")\n  endLine!: number;\n\n  @Column(\"text\")\n  code!: string;\n\n  @Column(\"text\")\n  unitType!: IndexUnitType;\n\n  @ManyToOne(() => IndexUnitEntity, (unit) => unit.children, {\n    nullable: true,\n    onDelete: \"CASCADE\",\n  })\n  @JoinColumn({ name: \"parent_id\" })\n  parent?: IndexUnitEntity | null;\n\n  @RelationId((unit: IndexUnitEntity) => unit.parent)\n  parentId?: string | null;\n\n  @OneToMany(() => IndexUnitEntity, (unit) => unit.parent, { nullable: true })\n  children?: IndexUnitEntity[];\n\n  @Column(\"simple-array\", { nullable: true })\n  embedding?: number[] | null;\n}\n","import path from \"path\";\nimport fs from \"fs/promises\";\nimport { DryScanServiceDeps } from \"./types\";\nimport { ExclusionService } from \"./ExclusionService\";\nimport { IndexUnit } from \"../types\";\nimport { EmbeddingService } from \"./EmbeddingService\";\nimport { FileEntity } from \"../db/entities/FileEntity\";\nimport { IndexUnitExtractor } from \"../IndexUnitExtractor\";\n\nexport interface InitOptions {\n  skipEmbeddings?: boolean;\n}\n\nexport class RepositoryInitializer {\n  constructor(\n    private readonly deps: DryScanServiceDeps,\n    private readonly exclusionService: ExclusionService\n  ) {}\n\n  async init(options?: InitOptions): Promise<void> {\n    const extractor = this.deps.extractor;\n\n    console.log(\"[DryScan] Phase 1/3: Extracting code units...\");\n    await this.initUnits(extractor);\n    console.log(\"[DryScan] Phase 2/3: Computing embeddings (may be slow)...\");\n    await this.computeEmbeddings(options?.skipEmbeddings === true);\n    console.log(\"[DryScan] Phase 3/3: Tracking files...\");\n    await this.trackFiles(extractor);\n    await this.exclusionService.cleanupExcludedFiles();\n    console.log(\"[DryScan] Initialization phases complete.\");\n  }\n\n  private async initUnits(extractor: IndexUnitExtractor): Promise<void> {\n    const units = await extractor.scan(this.deps.repoPath);\n    console.log(`[DryScan] Extracted ${units.length} index units.`);\n    await this.deps.db.saveUnits(units);\n  }\n\n  private async computeEmbeddings(skipEmbeddings: boolean): Promise<void> {\n    if (skipEmbeddings) {\n      console.log(\"[DryScan] Skipping embedding computation by request.\");\n      return;\n    }\n    const allUnits: IndexUnit[] = await this.deps.db.getAllUnits();\n    const total = allUnits.length;\n    console.log(`[DryScan] Computing embeddings for ${total} units...`);\n\n    const updated: IndexUnit[] = [];\n    const progressInterval = Math.max(1, Math.ceil(total / 10));\n    const embeddingService = new EmbeddingService(this.deps.repoPath);\n\n    for (let i = 0; i < total; i++) {\n      const unit = allUnits[i];\n      try {\n        const enriched = await embeddingService.addEmbedding(unit);\n        updated.push(enriched);\n      } catch (err: any) {\n        console.error(\n          `[DryScan] Embedding failed for ${unit.filePath} (${unit.name}): ${err?.message || err}`\n        );\n        throw err;\n      }\n\n      const completed = i + 1;\n      if (completed === total || completed % progressInterval === 0) {\n        const pct = Math.floor((completed / total) * 100);\n        console.log(`[DryScan] Embeddings ${completed}/${total} (${pct}%)`);\n      }\n    }\n\n    await this.deps.db.updateUnits(updated);\n  }\n\n  private async trackFiles(extractor: IndexUnitExtractor): Promise<void> {\n    const allFunctions = await extractor.listSourceFiles(this.deps.repoPath);\n    const fileEntities: FileEntity[] = [];\n\n    for (const relPath of allFunctions) {\n      const fullPath = path.join(this.deps.repoPath, relPath);\n      const stat = await fs.stat(fullPath);\n      const checksum = await extractor.computeChecksum(fullPath);\n\n      const fileEntity = new FileEntity();\n      fileEntity.filePath = relPath;\n      fileEntity.checksum = checksum;\n      fileEntity.mtime = stat.mtimeMs;\n      fileEntities.push(fileEntity);\n    }\n\n    await this.deps.db.saveFiles(fileEntities);\n    console.log(`[DryScan] Tracked ${fileEntities.length} files.`);\n  }\n}","import debug from \"debug\";\nimport { OllamaEmbeddings } from \"@langchain/ollama\";\nimport { HuggingFaceInferenceEmbeddings } from \"@langchain/community/embeddings/hf\";\nimport { IndexUnit } from \"../types\";\nimport { configStore } from \"../config/configStore\";\n\nconst log = debug(\"DryScan:EmbeddingService\");\n\n// Model names for each provider\nconst OLLAMA_MODEL = \"qwen3-embedding:0.6b\";\nconst HUGGINGFACE_MODEL = \"Qwen/Qwen3-Embedding-0.6B\";\n\nexport class EmbeddingService {\n    constructor(private readonly repoPath: string) { }\n\n    /**\n     * Generates an embedding for the given index unit using the configured provider.\n     * Skips embedding if code exceeds the configured context length.\n     */\n    async addEmbedding(fn: IndexUnit): Promise<IndexUnit> {\n        const config = await configStore.get(this.repoPath);\n        const maxContext = config?.contextLength ?? 2048;\n        if (fn.code.length > maxContext) {\n            log(\n                \"Skipping embedding for %s (code length %d exceeds context %d)\",\n                fn.id,\n                fn.code.length,\n                maxContext\n            );\n            return { ...fn, embedding: null };\n        }\n\n        const source = config.embeddingSource;\n        if (!source) {\n            const message = `Embedding source is not configured for repository at ${this.repoPath}`;\n            log(message);\n            throw new Error(message);\n        }\n\n        const embeddings = this.buildProvider(source);\n        const embedding = await embeddings.embedQuery(fn.code);\n        return { ...fn, embedding };\n    }\n\n    /**\n     * Builds the embedding provider based on the source configuration.\n     * - URL (http/https): Uses Ollama with \"embeddinggemma\" model\n     * - \"huggingface\": Uses HuggingFace Inference API with \"embeddinggemma-300m\" model\n     */\n    private buildProvider(source: string) {\n        // HuggingFace Inference API\n        if (source.toLowerCase() === \"huggingface\") {\n            log(\"Using HuggingFace Inference with model: %s\", HUGGINGFACE_MODEL);\n            return new HuggingFaceInferenceEmbeddings({\n                model: HUGGINGFACE_MODEL,\n                provider: \"hf-inference\",\n            });\n        }\n\n        // Ollama keyword or direct URL\n        const ollamaBaseUrl = this.resolveOllamaBaseUrl(source);\n        if (ollamaBaseUrl !== null) {\n            log(\"Using Ollama%s with model: %s\", ollamaBaseUrl ? ` at ${ollamaBaseUrl}` : \"\", OLLAMA_MODEL);\n            return new OllamaEmbeddings({ model: OLLAMA_MODEL, ...(ollamaBaseUrl && { baseUrl: ollamaBaseUrl }) });\n        }\n\n        const message = `Unsupported embedding source: ${source || \"(empty)\"}. Use \"huggingface\" or an Ollama URL.`;\n        log(message);\n        throw new Error(message);\n    }\n\n    /**\n     * Returns the Ollama base URL if source is an HTTP URL, undefined if source is \"ollama\" (use default),\n     * or null if source is not an Ollama provider at all.\n     */\n    private resolveOllamaBaseUrl(source: string): string | undefined | null {\n        if (/^https?:\\/\\//i.test(source)) return source;\n        if (source.toLowerCase() === \"ollama\") return undefined;\n        return null;\n    }\n}","import debug from \"debug\";\nimport { DryScanServiceDeps } from \"./types\";\nimport { ExclusionService } from \"./ExclusionService\";\nimport { performIncrementalUpdate } from \"../DryScanUpdater\";\nimport { DuplicationCache } from \"./DuplicationCache\";\n\nconst log = debug(\"DryScan:UpdateService\");\n\nexport class UpdateService {\n  constructor(\n    private readonly deps: DryScanServiceDeps,\n    private readonly exclusionService: ExclusionService\n  ) {}\n\n  async updateIndex(): Promise<void> {\n    const extractor = this.deps.extractor;\n    const cache = DuplicationCache.getInstance();\n\n    try {\n      const changeSet = await performIncrementalUpdate(this.deps.repoPath, extractor, this.deps.db);\n      await this.exclusionService.cleanupExcludedFiles();\n      await cache.invalidate([...changeSet.changed, ...changeSet.deleted]);\n    } catch (err) {\n      log(\"Error during index update:\", err);\n      throw err;\n    }\n  }\n}","import path from \"path\";\nimport fs from \"fs/promises\";\nimport debug from \"debug\";\nimport { IndexUnit } from \"./types\";\nimport { IndexUnitExtractor } from \"./IndexUnitExtractor\";\nimport { DryScanDatabase } from \"./db/DryScanDatabase\";\nimport { FileEntity } from \"./db/entities/FileEntity\";\nimport { EmbeddingService } from \"./services/EmbeddingService\";\n\nconst log = debug(\"DryScan:Updater\");\n\n/**\n * DryScan Updater Module\n * \n * This module contains all incremental update logic for DryScan.\n * Separated from DryScan.ts to keep that file focused on core operations.\n * \n * Represents the result of change detection.\n * Categorizes files into added, changed, deleted, and unchanged.\n */\nexport interface FileChangeSet {\n  added: string[];\n  changed: string[];\n  deleted: string[];\n  unchanged: string[];\n}\n\n/**\n * Detects which files have been added, changed, or deleted since last scan.\n * Uses mtime as fast check, then checksum for verification.\n * \n * @param repoPath - Root path of the repository\n * @param extractor - Index unit extractor instance for file operations\n * @param db - Database instance for retrieving tracked files\n * @returns Change set with categorized file paths\n */\nexport async function detectFileChanges(\n  repoPath: string,\n  extractor: IndexUnitExtractor,\n  db: DryScanDatabase\n): Promise<FileChangeSet> {\n  // Get current files in repository\n  const currentFiles = await extractor.listSourceFiles(repoPath);\n  const currentFileSet = new Set(currentFiles);\n\n  // Get tracked files from database\n  const trackedFiles = await db.getAllFiles();\n  const trackedFileMap = new Map(trackedFiles.map(f => [f.filePath, f]));\n\n  const added: string[] = [];\n  const changed: string[] = [];\n  const unchanged: string[] = [];\n\n  // Check each current file\n  for (const filePath of currentFiles) {\n    const tracked = trackedFileMap.get(filePath);\n    \n    if (!tracked) {\n      // New file\n      added.push(filePath);\n      continue;\n    }\n\n    // Check if file changed using mtime first (fast check)\n    const fullPath = path.join(repoPath, filePath);\n    const stat = await fs.stat(fullPath);\n    \n    if (stat.mtimeMs !== tracked.mtime) {\n      // Mtime changed, verify with checksum\n      const currentChecksum = await extractor.computeChecksum(fullPath);\n      if (currentChecksum !== tracked.checksum) {\n        changed.push(filePath);\n      } else {\n        // Mtime changed but content same\n        unchanged.push(filePath);\n      }\n    } else {\n      unchanged.push(filePath);\n    }\n  }\n\n  // Find deleted files\n  const deleted = trackedFiles\n    .map(f => f.filePath)\n    .filter(fp => !currentFileSet.has(fp));\n\n  return { added, changed, deleted, unchanged };\n}\n\n/**\n * Extracts index units from a list of files.\n * Used during incremental updates.\n * \n * @param filePaths - Array of relative file paths to extract from\n * @param extractor - Index unit extractor instance\n * @returns Array of extracted units\n */\nexport async function extractUnitsFromFiles(\n  filePaths: string[],\n  extractor: IndexUnitExtractor\n): Promise<IndexUnit[]> {\n  const allUnits: IndexUnit[] = [];\n  \n  for (const relPath of filePaths) {\n    const functions = await extractor.scan(relPath);\n    allUnits.push(...functions);\n  }\n  \n  return allUnits;\n}\n\n/**\n * Updates file tracking metadata after processing changes.\n * Removes deleted files, updates changed files, adds new files.\n * \n * @param changeSet - Set of file changes to apply\n * @param repoPath - Root path of the repository\n * @param extractor - Index unit extractor for checksum computation\n * @param db - Database instance for file tracking\n */\nexport async function updateFileTracking(\n  changeSet: FileChangeSet,\n  repoPath: string,\n  extractor: IndexUnitExtractor,\n  db: DryScanDatabase\n): Promise<void> {\n  // Remove deleted files\n  if (changeSet.deleted.length > 0) {\n    if (typeof (db as any).removeFilesByFilePaths === \"function\") {\n      await (db as any).removeFilesByFilePaths(changeSet.deleted);\n    } else if (typeof (db as any).removeFiles === \"function\") {\n      await (db as any).removeFiles(changeSet.deleted);\n    }\n  }\n\n  // Create file entities for new and changed files\n  const filesToTrack = [...changeSet.added, ...changeSet.changed];\n  if (filesToTrack.length > 0) {\n    const fileEntities: FileEntity[] = [];\n    \n    for (const relPath of filesToTrack) {\n      const fullPath = path.join(repoPath, relPath);\n      const stat = await fs.stat(fullPath);\n      const checksum = await extractor.computeChecksum(fullPath);\n      \n      const fileEntity = new FileEntity();\n      fileEntity.filePath = relPath;\n      fileEntity.checksum = checksum;\n      fileEntity.mtime = stat.mtimeMs;\n      \n      fileEntities.push(fileEntity);\n    }\n    \n    await db.saveFiles(fileEntities);\n  }\n}\n\n/**\n * Performs incremental update of the DryScan index.\n * Detects file changes and reprocesses only affected files.\n * \n * @param repoPath - Root path of the repository\n * @param extractor - Index unit extractor instance\n * @param db - Database instance (must be initialized)\n */\nexport async function performIncrementalUpdate(\n  repoPath: string,\n  extractor: IndexUnitExtractor,\n  db: DryScanDatabase,\n): Promise<FileChangeSet> {\n  log(\"Starting incremental update\");\n  const embeddingService = new EmbeddingService(repoPath);\n  \n  // Step 1: Detect changes\n  const changeSet = await detectFileChanges(repoPath, extractor, db);\n  \n  if (changeSet.changed.length === 0 && \n      changeSet.added.length === 0 && \n      changeSet.deleted.length === 0) {\n    log(\"No changes detected. Index is up to date.\");\n    return changeSet;\n  }\n\n  log(`Changes detected: ${changeSet.added.length} added, ${changeSet.changed.length} changed, ${changeSet.deleted.length} deleted`);\n\n  // Step 2: Remove old data for changed/deleted files\n  const filesToRemove = [...changeSet.changed, ...changeSet.deleted];\n  if (filesToRemove.length > 0) {\n      await db.removeUnitsByFilePaths(filesToRemove);\n      log(`Removed units from ${filesToRemove.length} files`);\n  }\n\n  // Step 3: Extract functions from new/changed files\n  const filesToProcess = [...changeSet.added, ...changeSet.changed];\n  if (filesToProcess.length > 0) {\n    const newUnits = await extractUnitsFromFiles(filesToProcess, extractor);\n      await db.saveUnits(newUnits);\n      log(`Extracted and saved ${newUnits.length} units from ${filesToProcess.length} files`);\n\n    // Step 4: Recompute embeddings for affected units only\n    const total = newUnits.length;\n    if (total > 0) {\n      log(`Recomputing embeddings for ${total} units`);\n      const progressInterval = Math.max(1, Math.ceil(total / 10));\n      const updatedWithEmbeddings = [] as IndexUnit[];\n\n      for (let i = 0; i < total; i++) {\n        const unit = newUnits[i];\n        try {\n          const enriched = await embeddingService.addEmbedding(unit);\n          updatedWithEmbeddings.push(enriched);\n        } catch (err: any) {\n          console.error(\n            `[DryScan] embedding failed for ${unit.filePath} (${unit.name}): ${err?.message || err}`\n          );\n          throw err;\n        }\n\n        const completed = i + 1;\n        if (completed === total || completed % progressInterval === 0) {\n          const pct = Math.floor((completed / total) * 100);\n          console.log(`[DryScan] Incremental embeddings ${completed}/${total} (${pct}%)`);\n        }\n      }\n\n      await db.updateUnits(updatedWithEmbeddings);\n      log(`Recomputed embeddings for ${updatedWithEmbeddings.length} units`);\n    }\n  }\n\n  // Step 5: Update file tracking\n  await updateFileTracking(changeSet, repoPath, extractor, db);\n  log(\"Incremental update complete\");\n\n  return changeSet;\n}\n","import { DuplicateGroup } from \"../types\";\n\n/**\n * In-memory cache for duplicate comparison scores.\n * Stores a global map of comparison keys and a per-file index for fast invalidation.\n */\nexport class DuplicationCache {\n  private static instance: DuplicationCache | null = null;\n\n  private readonly comparisons = new Map<string, number>();\n  private readonly fileIndex = new Map<string, Set<string>>();\n  private initialized = false;\n\n  static getInstance(): DuplicationCache {\n    if (!DuplicationCache.instance) {\n      DuplicationCache.instance = new DuplicationCache();\n    }\n    return DuplicationCache.instance;\n  }\n\n  /**\n   * Updates the cache with fresh duplicate groups. Not awaited by callers to avoid blocking.\n   */\n  async update(groups: DuplicateGroup[]): Promise<void> {\n    if (!groups) return;\n\n    for (const group of groups) {\n      const key = this.makeKey(group.left.id, group.right.id);\n      this.comparisons.set(key, group.similarity);\n      this.addKeyForFile(group.left.filePath, key);\n      this.addKeyForFile(group.right.filePath, key);\n    }\n\n    this.initialized = this.initialized || groups.length > 0;\n  }\n\n  /**\n   * Retrieves a cached similarity if present and valid for both file paths.\n   * Returns null when the cache has not been initialized or when the pair is missing.\n   */\n  get(leftId: string, rightId: string, leftFilePath: string, rightFilePath: string): number | null {\n    if (!this.initialized) return null;\n\n    const key = this.makeKey(leftId, rightId);\n    if (!this.fileHasKey(leftFilePath, key) || !this.fileHasKey(rightFilePath, key)) {\n      return null;\n    }\n\n    const value = this.comparisons.get(key);\n    return typeof value === \"number\" ? value : null;\n  }\n\n  /**\n   * Invalidates all cached comparisons involving the provided file paths.\n   */\n  async invalidate(paths: string[]): Promise<void> {\n    if (!this.initialized || !paths || paths.length === 0) return;\n\n    const unique = new Set(paths);\n    for (const filePath of unique) {\n      const keys = this.fileIndex.get(filePath);\n      if (!keys) continue;\n\n      for (const key of keys) {\n        this.comparisons.delete(key);\n        for (const [otherPath, otherKeys] of this.fileIndex.entries()) {\n          if (otherKeys.delete(key) && otherKeys.size === 0) {\n            this.fileIndex.delete(otherPath);\n          }\n        }\n      }\n\n      this.fileIndex.delete(filePath);\n    }\n\n    if (this.comparisons.size === 0) {\n      this.initialized = false;\n    }\n  }\n\n  /**\n   * Clears all cached data. Intended for test setup.\n   */\n  clear(): void {\n    this.comparisons.clear();\n    this.fileIndex.clear();\n    this.initialized = false;\n  }\n\n  private addKeyForFile(filePath: string, key: string): void {\n    const current = this.fileIndex.get(filePath) ?? new Set<string>();\n    current.add(key);\n    this.fileIndex.set(filePath, current);\n  }\n\n  private fileHasKey(filePath: string, key: string): boolean {\n    const keys = this.fileIndex.get(filePath);\n    return keys ? keys.has(key) : false;\n  }\n\n  private makeKey(leftId: string, rightId: string): string {\n    return [leftId, rightId].sort().join(\"::\");\n  }\n}\n","import debug from \"debug\";\nimport shortUuid from \"short-uuid\";\nimport { cosineSimilarity } from \"@langchain/core/utils/math\";\nimport { DryScanServiceDeps } from \"./types\";\nimport { DuplicateAnalysisResult, DuplicateGroup, DuplicationScore, IndexUnit, IndexUnitType } from \"../types\";\nimport { indexConfig } from \"../config/indexConfig\";\nimport { DryConfig } from \"../types\";\nimport { DuplicationCache } from \"./DuplicationCache\";\n\nconst log = debug(\"DryScan:DuplicateService\");\n\nexport class DuplicateService {\n  private config?: DryConfig;\n  private readonly cache = DuplicationCache.getInstance();\n\n  constructor(private readonly deps: DryScanServiceDeps) {}\n\n  //todo vetter optimisation\n  async findDuplicates(config: DryConfig): Promise<DuplicateAnalysisResult> {\n    this.config = config;\n    const t0 = performance.now();\n    const allUnits = await this.deps.db.getAllUnits();\n    log(\"Starting duplicate analysis on %d units\", allUnits.length);\n    if (allUnits.length < 2) {\n      log(\"Not enough units to compare, returning empty result\");\n      const score = this.computeDuplicationScore([], allUnits);\n      return { duplicates: [], score };\n    }\n\n    const thresholds = this.resolveThresholds(config.threshold);\n    log(\"Resolved thresholds: function=%d, block=%d, class=%d\", thresholds.function, thresholds.block, thresholds.class);\n    const duplicates = this.computeDuplicates(allUnits, thresholds);\n    const filteredDuplicates = duplicates.filter((group) => !this.isGroupExcluded(group));\n    log(\"Found %d duplicate groups (%d excluded)\", filteredDuplicates.length, duplicates.length - filteredDuplicates.length);\n\n    // Update cache asynchronously; no need to block the main flow.\n    this.cache.update(filteredDuplicates).catch((err) => log(\"Cache update failed: %O\", err));\n\n    const score = this.computeDuplicationScore(filteredDuplicates, allUnits);\n    log(\"findDuplicates completed in %dms\", (performance.now() - t0).toFixed(2));\n    return { duplicates: filteredDuplicates, score };\n  }\n\n  private resolveThresholds(functionThreshold?: number): { function: number; block: number; class: number } {\n    const defaults = indexConfig.thresholds;\n    const clamp = (value: number) => Math.min(1, Math.max(0, value));\n\n    const base = functionThreshold ?? defaults.function;\n    const blockOffset = defaults.block - defaults.function;\n    const classOffset = defaults.class - defaults.function;\n\n    const functionThresholdValue = clamp(base);\n    return {\n      function: functionThresholdValue,\n      block: clamp(functionThresholdValue + blockOffset),\n      class: clamp(functionThresholdValue + classOffset),\n    };\n  }\n\n  private computeDuplicates(\n    units: IndexUnit[],\n    thresholds: { function: number; block: number; class: number }\n  ): DuplicateGroup[] {\n    const duplicates: DuplicateGroup[] = [];\n    const byType = new Map<IndexUnitType, IndexUnit[]>();\n\n    for (const unit of units) {\n      const list = byType.get(unit.unitType) ?? [];\n      list.push(unit);\n      byType.set(unit.unitType, list);\n    }\n\n    const t0 = performance.now();\n\n    for (const [type, typedUnits] of byType.entries()) {\n      const threshold = this.getThreshold(type, thresholds);\n      log(\"Comparing %d units of type '%s' with threshold %d\", typedUnits.length, type, threshold);\n      const typeStart = performance.now();\n\n      for (let i = 0; i < typedUnits.length; i++) {\n        for (let j = i + 1; j < typedUnits.length; j++) {\n          const left = typedUnits[i];\n          const right = typedUnits[j];\n\n          if (this.shouldSkipComparison(left, right)) {\n            log(\"Skipping nested block comparison: '%s' and '%s'\", left.name, right.name);\n            continue;\n          }\n\n          const cached = this.cache.get(left.id, right.id, left.filePath, right.filePath);\n          let similarity: number | null = null;\n\n          if (cached !== null) {\n            log(\"Cache hit for '%s' <-> '%s': similarity=%d\", left.name, right.name, cached);\n            similarity = cached;\n          } else {\n            if (!left.embedding || !right.embedding) {\n              log(\"Skipping '%s' <-> '%s': missing embedding\", left.name, right.name);\n              continue;\n            }\n            similarity = this.computeWeightedSimilarity(left, right);\n            log(\"Computed similarity for '%s' <-> '%s': %d\", left.name, right.name, similarity);\n          }\n\n          if (similarity === null) continue;\n\n          if (similarity >= threshold) {\n            const exclusionString = this.deps.pairing.pairKeyForUnits(left, right);\n            if (!exclusionString) continue;\n\n            log(\"Duplicate found: '%s' <-> '%s' (similarity=%d)\", left.name, right.name, similarity);\n            duplicates.push({\n              id: `${left.id}::${right.id}`,\n              similarity,\n              shortId: shortUuid.generate(),\n              exclusionString,\n              left: {\n                id: left.id,\n                name: left.name,\n                filePath: left.filePath,\n                startLine: left.startLine,\n                endLine: left.endLine,\n                code: left.code,\n                unitType: left.unitType,\n              },\n              right: {\n                id: right.id,\n                name: right.name,\n                filePath: right.filePath,\n                startLine: right.startLine,\n                endLine: right.endLine,\n                code: right.code,\n                unitType: right.unitType,\n              },\n            });\n          }\n        }\n      }\n      log(\"Type '%s' comparisons completed in %dms\", type, (performance.now() - typeStart).toFixed(2));\n    }\n\n    log(\"computeDuplicates completed in %dms, found %d raw duplicates\", (performance.now() - t0).toFixed(2), duplicates.length);\n    return duplicates.sort((a, b) => b.similarity - a.similarity);\n  }\n\n  private isGroupExcluded(group: DuplicateGroup): boolean {\n    const config = this.config;\n    if (!config || !config.excludedPairs || config.excludedPairs.length === 0) return false;\n    const key = this.deps.pairing.pairKeyForUnits(group.left, group.right);\n    if (!key) return false;\n    const actual = this.deps.pairing.parsePairKey(key);\n    if (!actual) return false;\n    return config.excludedPairs.some((entry) => {\n      const parsed = this.deps.pairing.parsePairKey(entry);\n      return parsed ? this.deps.pairing.pairKeyMatches(actual, parsed) : false;\n    });\n  }\n\n  private getThreshold(type: IndexUnitType, thresholds: { function: number; block: number; class: number }): number {\n    if (type === IndexUnitType.CLASS) return thresholds.class;\n    if (type === IndexUnitType.BLOCK) return thresholds.block;\n    return thresholds.function;\n  }\n\n  private computeWeightedSimilarity(left: IndexUnit, right: IndexUnit): number {\n    const selfSimilarity = this.similarityWithFallback(left, right);\n\n    if (left.unitType === IndexUnitType.CLASS) {\n      return selfSimilarity * indexConfig.weights.class.self;\n    }\n\n    if (left.unitType === IndexUnitType.FUNCTION) {\n      const weights = indexConfig.weights.function;\n      const hasParentClass = !!this.findParentOfType(left, IndexUnitType.CLASS) && !!this.findParentOfType(right, IndexUnitType.CLASS);\n      const parentClassSimilarity = hasParentClass ? this.parentSimilarity(left, right, IndexUnitType.CLASS) : 0;\n\n      // Re-normalize weights when parent context is missing, so standalone units aren't penalized.\n      const totalWeight = weights.self + (hasParentClass ? weights.parentClass : 0);\n      return ((weights.self * selfSimilarity) + (hasParentClass ? (weights.parentClass * parentClassSimilarity) : 0)) / totalWeight;\n    }\n\n    const weights = indexConfig.weights.block;\n    const hasParentFunction = !!this.findParentOfType(left, IndexUnitType.FUNCTION) && !!this.findParentOfType(right, IndexUnitType.FUNCTION);\n    const hasParentClass = !!this.findParentOfType(left, IndexUnitType.CLASS) && !!this.findParentOfType(right, IndexUnitType.CLASS);\n    const parentFuncSim = hasParentFunction ? this.parentSimilarity(left, right, IndexUnitType.FUNCTION) : 0;\n    const parentClassSim = hasParentClass ? this.parentSimilarity(left, right, IndexUnitType.CLASS) : 0;\n\n    // Re-normalize weights when some parent context is missing.\n    const totalWeight =\n      weights.self +\n      (hasParentFunction ? weights.parentFunction : 0) +\n      (hasParentClass ? weights.parentClass : 0);\n\n    return (\n      (weights.self * selfSimilarity) +\n      (hasParentFunction ? (weights.parentFunction * parentFuncSim) : 0) +\n      (hasParentClass ? (weights.parentClass * parentClassSim) : 0)\n    ) / totalWeight;\n  }\n\n  private parentSimilarity(left: IndexUnit, right: IndexUnit, targetType: IndexUnitType): number {\n    const leftParent = this.findParentOfType(left, targetType);\n    const rightParent = this.findParentOfType(right, targetType);\n    if (!leftParent || !rightParent) return 0;\n    return this.similarityWithFallback(leftParent, rightParent);\n  }\n\n  private similarityWithFallback(left: IndexUnit, right: IndexUnit): number {\n    const leftHasEmbedding = this.hasVector(left);\n    const rightHasEmbedding = this.hasVector(right);\n\n    if (leftHasEmbedding && rightHasEmbedding) {\n      return cosineSimilarity([left.embedding as number[]], [right.embedding as number[]])[0][0];\n    }\n\n    return this.childSimilarity(left, right);\n  }\n\n  private childSimilarity(left: IndexUnit, right: IndexUnit): number {\n    const leftChildren = left.children ?? [];\n    const rightChildren = right.children ?? [];\n    if (leftChildren.length === 0 || rightChildren.length === 0) return 0;\n\n    let best = 0;\n    for (const lChild of leftChildren) {\n      for (const rChild of rightChildren) {\n        if (lChild.unitType !== rChild.unitType) continue;\n        const sim = this.similarityWithFallback(lChild, rChild);\n        if (sim > best) best = sim;\n      }\n    }\n    return best;\n  }\n\n  private hasVector(unit: IndexUnit): boolean {\n    return Array.isArray(unit.embedding) && unit.embedding.length > 0;\n  }\n\n  private shouldSkipComparison(left: IndexUnit, right: IndexUnit): boolean {\n    if (left.unitType !== IndexUnitType.BLOCK || right.unitType !== IndexUnitType.BLOCK) {\n      return false;\n    }\n\n    if (left.filePath !== right.filePath) {\n      return false;\n    }\n\n    const leftContainsRight = left.startLine <= right.startLine && left.endLine >= right.endLine;\n    const rightContainsLeft = right.startLine <= left.startLine && right.endLine >= left.endLine;\n    return leftContainsRight || rightContainsLeft;\n  }\n\n  private findParentOfType(unit: IndexUnit, targetType: IndexUnitType): IndexUnit | null {\n    let current: IndexUnit | undefined | null = unit.parent;\n    while (current) {\n      if (current.unitType === targetType) return current;\n      current = current.parent;\n    }\n    return null;\n  }\n\n  private computeDuplicationScore(duplicates: DuplicateGroup[], allUnits: IndexUnit[]): DuplicationScore {\n    const totalLines = this.calculateTotalLines(allUnits);\n\n    if (totalLines === 0 || duplicates.length === 0) {\n      return {\n        score: 0,\n        grade: \"Excellent\",\n        totalLines,\n        duplicateLines: 0,\n        duplicateGroups: 0,\n      };\n    }\n\n    const weightedDuplicateLines = duplicates.reduce((sum, group) => {\n      const leftLines = group.left.endLine - group.left.startLine + 1;\n      const rightLines = group.right.endLine - group.right.startLine + 1;\n      const avgLines = (leftLines + rightLines) / 2;\n      return sum + group.similarity * avgLines;\n    }, 0);\n\n    const score = (weightedDuplicateLines / totalLines) * 100;\n    const grade = this.getScoreGrade(score);\n\n    return {\n      score,\n      grade,\n      totalLines,\n      duplicateLines: Math.round(weightedDuplicateLines),\n      duplicateGroups: duplicates.length,\n    };\n  }\n\n  private calculateTotalLines(units: IndexUnit[]): number {\n    return units.reduce((sum, unit) => {\n      const lines = unit.endLine - unit.startLine + 1;\n      return sum + lines;\n    }, 0);\n  }\n\n  private getScoreGrade(score: number): DuplicationScore[\"grade\"] {\n    if (score < 5) return \"Excellent\";\n    if (score < 15) return \"Good\";\n    if (score < 30) return \"Fair\";\n    if (score < 50) return \"Poor\";\n    return \"Critical\";\n  }\n}","import { DryConfig } from \"../types\";\nimport { configStore } from \"../config/configStore\";\nimport { DryScanServiceDeps } from \"./types\";\nimport { IndexUnitType } from \"../types\";\nimport { minimatch } from \"minimatch\";\nimport { ParsedPairKey } from \"./PairingService\";\n\nexport class ExclusionService {\n  private config?: DryConfig;\n\n  constructor(private readonly deps: DryScanServiceDeps) {}\n\n  async cleanupExcludedFiles(): Promise<void> {\n    const config = await this.loadConfig();\n    if (!config.excludedPaths || config.excludedPaths.length === 0) return;\n\n    const units = await this.deps.db.getAllUnits();\n    const files = await this.deps.db.getAllFiles();\n\n    const unitPathsToRemove = new Set<string>();\n    for (const unit of units) {\n      if (this.pathExcluded(unit.filePath)) {\n        unitPathsToRemove.add(unit.filePath);\n      }\n    }\n\n    const filePathsToRemove = new Set<string>();\n    for (const file of files) {\n      if (this.pathExcluded(file.filePath)) {\n        filePathsToRemove.add(file.filePath);\n      }\n    }\n\n    const paths = [...new Set([...unitPathsToRemove, ...filePathsToRemove])];\n    if (paths.length > 0) {\n      await this.deps.db.removeUnitsByFilePaths(paths);\n      await this.deps.db.removeFilesByFilePaths(paths);\n    }\n  }\n\n  async cleanExclusions(): Promise<{ removed: number; kept: number }> {\n    const config = await this.loadConfig();\n    const units = await this.deps.db.getAllUnits();\n\n    const actualPairsByType = {\n      [IndexUnitType.CLASS]: this.buildPairKeys(units, IndexUnitType.CLASS),\n      [IndexUnitType.FUNCTION]: this.buildPairKeys(units, IndexUnitType.FUNCTION),\n      [IndexUnitType.BLOCK]: this.buildPairKeys(units, IndexUnitType.BLOCK),\n    };\n\n    const kept: string[] = [];\n    const removed: string[] = [];\n\n    for (const entry of config.excludedPairs || []) {\n      const parsed = this.deps.pairing.parsePairKey(entry);\n      if (!parsed) {\n        removed.push(entry);\n        continue;\n      }\n\n      const candidates = actualPairsByType[parsed.type];\n      const matched = candidates.some((actual) => this.deps.pairing.pairKeyMatches(actual, parsed));\n      if (matched) {\n        kept.push(entry);\n      } else {\n        removed.push(entry);\n      }\n    }\n\n    const nextConfig: DryConfig = { ...config, excludedPairs: kept };\n    await configStore.save(this.deps.repoPath, nextConfig);\n    this.config = nextConfig;\n\n    return { removed: removed.length, kept: kept.length };\n  }\n\n  private pathExcluded(filePath: string): boolean {\n    const config = this.config;\n    if (!config || !config.excludedPaths || config.excludedPaths.length === 0) return false;\n    return config.excludedPaths.some((pattern) => minimatch(filePath, pattern, { dot: true }));\n  }\n\n  private buildPairKeys(units: any[], type: IndexUnitType): ParsedPairKey[] {\n    const typed = units.filter((u) => u.unitType === type);\n    const pairs: ParsedPairKey[] = [];\n    for (let i = 0; i < typed.length; i++) {\n      for (let j = i + 1; j < typed.length; j++) {\n        const key = this.deps.pairing.pairKeyForUnits(typed[i], typed[j]);\n        const parsed = key ? this.deps.pairing.parsePairKey(key) : null;\n        if (parsed) {\n          pairs.push(parsed);\n        }\n      }\n    }\n    return pairs;\n  }\n\n  private async loadConfig(): Promise<DryConfig> {\n    this.config = await configStore.get(this.deps.repoPath);\n    return this.config;\n  }\n}","import crypto from \"node:crypto\";\nimport debug from \"debug\";\nimport { minimatch } from \"minimatch\";\nimport { LanguageExtractor } from \"../extractors/LanguageExtractor\";\nimport { IndexUnitExtractor } from \"../IndexUnitExtractor\";\nimport { IndexUnit, IndexUnitType } from \"../types\";\nimport { BLOCK_HASH_ALGO } from \"../const\";\n\nconst log = debug(\"DryScan:pairs\");\n\ntype UnitLike = Pick<IndexUnit, \"unitType\" | \"filePath\" | \"name\" | \"code\">;\n\nexport interface ParsedPairKey {\n  type: IndexUnitType;\n  left: string;\n  right: string;\n  key: string;\n}\n\n/**\n * Service for building and parsing pair keys with extractor-aware labeling.\n */\nexport class PairingService {\n  constructor(private readonly indexUnitExtractor: IndexUnitExtractor) {}\n\n  /**\n   * Creates a stable, order-independent key for two units of the same type.\n   * Returns null when units differ in type so callers can skip invalid pairs.\n   */\n  pairKeyForUnits(left: UnitLike, right: UnitLike): string | null {\n    if (left.unitType !== right.unitType) {\n      log(\"Skipping pair with mismatched types: %s vs %s\", left.unitType, right.unitType);\n      return null;\n    }\n    const type = left.unitType;\n    const leftLabel = this.unitLabel(left);\n    const rightLabel = this.unitLabel(right);\n    const [a, b] = [leftLabel, rightLabel].sort();\n    return `${type}|${a}|${b}`;\n  }\n\n  /**\n   * Parses a raw pair key into its components, returning null for malformed values.\n   * Sorting is applied so callers can compare pairs without worrying about order.\n   */\n  parsePairKey(value: string): ParsedPairKey | null {\n    const parts = value.split(\"|\");\n    if (parts.length !== 3) {\n      log(\"Invalid pair key format: %s\", value);\n      return null;\n    }\n    const [typeRaw, leftRaw, rightRaw] = parts;\n    const type = this.stringToUnitType(typeRaw);\n    if (!type) {\n      log(\"Unknown unit type in pair key: %s\", typeRaw);\n      return null;\n    }\n    const [left, right] = [leftRaw, rightRaw].sort();\n    return { type, left, right, key: `${type}|${left}|${right}` };\n  }\n\n  /**\n   * Checks whether an actual pair key satisfies a pattern, with glob matching for class paths.\n   */\n  pairKeyMatches(actual: ParsedPairKey, pattern: ParsedPairKey): boolean {\n    if (actual.type !== pattern.type) return false;\n    if (actual.type === IndexUnitType.CLASS) {\n      // Allow glob matching for class file paths.\n      const forward =\n        minimatch(actual.left, pattern.left, { dot: true }) &&\n        minimatch(actual.right, pattern.right, { dot: true });\n      const swapped =\n        minimatch(actual.left, pattern.right, { dot: true }) &&\n        minimatch(actual.right, pattern.left, { dot: true });\n      return forward || swapped;\n    }\n\n    // Functions and blocks use exact matching on canonical strings.\n    return (\n      (actual.left === pattern.left && actual.right === pattern.right) ||\n      (actual.left === pattern.right && actual.right === pattern.left)\n    );\n  }\n\n  /**\n   * Derives a reversible, extractor-aware label for a unit.\n   * Extractors may override; fallback uses a fixed format per unit type.\n   */\n  unitLabel(unit: UnitLike): string {\n    const extractor = this.findExtractor(unit.filePath);\n    const customLabel = extractor?.unitLabel?.(unit as IndexUnit);\n    if (customLabel) return customLabel;\n\n    switch (unit.unitType) {\n      case IndexUnitType.CLASS:\n        return unit.filePath;\n      case IndexUnitType.FUNCTION:\n        return this.canonicalFunctionSignature(unit);\n      case IndexUnitType.BLOCK:\n        return this.normalizedBlockHash(unit);\n      default:\n        return unit.name;\n    }\n  }\n\n  private findExtractor(filePath: string): LanguageExtractor | undefined {\n    return this.indexUnitExtractor.extractors.find((ex) => ex.supports(filePath));\n  }\n\n  private canonicalFunctionSignature(unit: UnitLike): string {\n    const arity = this.extractArity(unit.code);\n    return `${unit.name}(arity:${arity})`;\n  }\n\n  /**\n   * Normalizes block code (strips comments/whitespace) and hashes it for pair matching.\n   */\n  private normalizedBlockHash(unit: UnitLike): string {\n    const normalized = this.normalizeCode(unit.code);\n    return crypto.createHash(BLOCK_HASH_ALGO).update(normalized).digest(\"hex\");\n  }\n\n  private stringToUnitType(value: string): IndexUnitType | null {\n    if (value === IndexUnitType.CLASS) return IndexUnitType.CLASS;\n    if (value === IndexUnitType.FUNCTION) return IndexUnitType.FUNCTION;\n    if (value === IndexUnitType.BLOCK) return IndexUnitType.BLOCK;\n    return null;\n  }\n\n  private extractArity(code: string): number {\n    const match = code.match(/^[^{]*?\\(([^)]*)\\)/s);\n    if (!match) return 0;\n    const params = match[1]\n      .split(\",\")\n      .map((p) => p.trim())\n      .filter(Boolean);\n    return params.length;\n  }\n\n  private normalizeCode(code: string): string {\n    const withoutBlockComments = code.replace(/\\/\\*[\\s\\S]*?\\*\\//g, \"\");\n    const withoutLineComments = withoutBlockComments.replace(/\\/\\/[^\\n\\r]*/g, \"\");\n    return withoutLineComments.replace(/\\s+/g, \"\");\n  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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@goshenkata/dryscan-core",
-  "version": "1.2.4",
+  "version": "1.2.5",
   "description": "Core library for DryScan - semantic code duplication analyzer",
   "type": "module",
   "main": "./dist/index.js",

package/src/db/DryScanDatabase.ts

@@ -48,7 +48,7 @@ export class DryScanDatabase {
 
   async getUnit(id: string): Promise<IndexUnit | null> {
     if (!this.unitRepository) throw new Error("Database not initialized");
-    return this.unitRepository.findOne({ 
+    return this.unitRepository.findOne({
       where: { id },
       relations: ["children", "parent"]
     });

package/src/extractors/java.ts

@@ -233,6 +233,7 @@ export class JavaExtractor implements LanguageExtractor {
       filePath: file,
       startLine,
       endLine,
+      children: [],
       code: this.stripComments(source.slice(node.startIndex, node.endIndex)),
       unitType: IndexUnitType.FUNCTION,
       parentId: parentClass?.id,
@@ -274,9 +275,11 @@ export class JavaExtractor implements LanguageExtractor {
             parentId: parentFunction.id,
             parent: parentFunction,
           };
+          const contextLength = this.config?.contextLength ?? 2048;
+          const splitBlocks = this.textSplitBlockIfOverContextLimit(blockUnit, contextLength);
           parentFunction.children = parentFunction.children || [];
-          parentFunction.children.push(blockUnit);
-          blocks.push(blockUnit);
+          parentFunction.children.push(...splitBlocks);
+          blocks.push(...splitBlocks);
         }
       }
 
@@ -334,8 +337,25 @@ export class JavaExtractor implements LanguageExtractor {
     return withoutBlockComments.replace(/\/\/[^\n\r]*/g, "");
   }
 
-private removeDuplicates(units: IndexUnit[]): IndexUnit[] | PromiseLike<IndexUnit[]> {
-  return Array.from(new Map(units.map(u => [u.id, u])).values());
-}
+  private removeDuplicates(units: IndexUnit[]): IndexUnit[] | PromiseLike<IndexUnit[]> {
+    return Array.from(new Map(units.map(u => [u.id, u])).values());
+  }
+
+  /** Splits a block unit's code into chunks if it exceeds the context length limit. */
+  private textSplitBlockIfOverContextLimit(unit: IndexUnit, contextLength: number): IndexUnit[] {
+    if (unit.code.length <= contextLength) return [unit];
+
+    const chunks: IndexUnit[] = [];
+    let chunkIndex = 0;
+    for (let i = 0; i < unit.code.length; i += contextLength) {
+      chunks.push({
+        ...unit,
+        id: `${unit.id}:chunk${chunkIndex}`,
+        code: unit.code.slice(i, i + contextLength),
+      });
+      chunkIndex++;
+    }
+    return chunks;
+  }
 }
 

package/src/services/DuplicateService.ts

@@ -15,23 +15,29 @@ export class DuplicateService {
 
   constructor(private readonly deps: DryScanServiceDeps) {}
 
+  //todo vetter optimisation
   async findDuplicates(config: DryConfig): Promise<DuplicateAnalysisResult> {
     this.config = config;
+    const t0 = performance.now();
     const allUnits = await this.deps.db.getAllUnits();
+    log("Starting duplicate analysis on %d units", allUnits.length);
     if (allUnits.length < 2) {
+      log("Not enough units to compare, returning empty result");
       const score = this.computeDuplicationScore([], allUnits);
       return { duplicates: [], score };
     }
 
     const thresholds = this.resolveThresholds(config.threshold);
+    log("Resolved thresholds: function=%d, block=%d, class=%d", thresholds.function, thresholds.block, thresholds.class);
     const duplicates = this.computeDuplicates(allUnits, thresholds);
     const filteredDuplicates = duplicates.filter((group) => !this.isGroupExcluded(group));
-    log("Found %d duplicate groups", filteredDuplicates.length);
+    log("Found %d duplicate groups (%d excluded)", filteredDuplicates.length, duplicates.length - filteredDuplicates.length);
 
     // Update cache asynchronously; no need to block the main flow.
     this.cache.update(filteredDuplicates).catch((err) => log("Cache update failed: %O", err));
 
     const score = this.computeDuplicationScore(filteredDuplicates, allUnits);
+    log("findDuplicates completed in %dms", (performance.now() - t0).toFixed(2));
     return { duplicates: filteredDuplicates, score };
   }
 
@@ -64,24 +70,36 @@ export class DuplicateService {
       byType.set(unit.unitType, list);
     }
 
+    const t0 = performance.now();
+
     for (const [type, typedUnits] of byType.entries()) {
       const threshold = this.getThreshold(type, thresholds);
+      log("Comparing %d units of type '%s' with threshold %d", typedUnits.length, type, threshold);
+      const typeStart = performance.now();
 
       for (let i = 0; i < typedUnits.length; i++) {
         for (let j = i + 1; j < typedUnits.length; j++) {
           const left = typedUnits[i];
           const right = typedUnits[j];
 
-          if (this.shouldSkipComparison(left, right)) continue;
+          if (this.shouldSkipComparison(left, right)) {
+            log("Skipping nested block comparison: '%s' and '%s'", left.name, right.name);
+            continue;
+          }
 
           const cached = this.cache.get(left.id, right.id, left.filePath, right.filePath);
           let similarity: number | null = null;
 
           if (cached !== null) {
+            log("Cache hit for '%s' <-> '%s': similarity=%d", left.name, right.name, cached);
             similarity = cached;
           } else {
-            if (!left.embedding || !right.embedding) continue;
+            if (!left.embedding || !right.embedding) {
+              log("Skipping '%s' <-> '%s': missing embedding", left.name, right.name);
+              continue;
+            }
             similarity = this.computeWeightedSimilarity(left, right);
+            log("Computed similarity for '%s' <-> '%s': %d", left.name, right.name, similarity);
           }
 
           if (similarity === null) continue;
@@ -90,6 +108,7 @@ export class DuplicateService {
             const exclusionString = this.deps.pairing.pairKeyForUnits(left, right);
             if (!exclusionString) continue;
 
+            log("Duplicate found: '%s' <-> '%s' (similarity=%d)", left.name, right.name, similarity);
             duplicates.push({
               id: `${left.id}::${right.id}`,
               similarity,
@@ -117,8 +136,10 @@ export class DuplicateService {
           }
         }
       }
+      log("Type '%s' comparisons completed in %dms", type, (performance.now() - typeStart).toFixed(2));
     }
 
+    log("computeDuplicates completed in %dms, found %d raw duplicates", (performance.now() - t0).toFixed(2), duplicates.length);
     return duplicates.sort((a, b) => b.similarity - a.similarity);
   }