neuronlayer 0.1.9 → 0.2.0

package/src/storage/tier2.ts

@@ -1,972 +0,0 @@
-import type Database from 'better-sqlite3';
-import type { FileMetadata, Decision, SearchResult, DependencyRelation, CodeSymbol, Import, Export, SymbolKind } from '../types/index.js';
-
-export class Tier2Storage {
-  private db: Database.Database;
-
-  constructor(db: Database.Database) {
-    this.db = db;
-  }
-
-  // File operations
-  upsertFile(
-    path: string,
-    contentHash: string,
-    preview: string,
-    language: string,
-    sizeBytes: number,
-    lineCount: number,
-    lastModified: number
-  ): number {
-    const stmt = this.db.prepare(`
-      INSERT INTO files (path, content_hash, preview, language, size_bytes, line_count, last_modified, indexed_at)
-      VALUES (?, ?, ?, ?, ?, ?, ?, unixepoch())
-      ON CONFLICT(path) DO UPDATE SET
-        content_hash = excluded.content_hash,
-        preview = excluded.preview,
-        language = excluded.language,
-        size_bytes = excluded.size_bytes,
-        line_count = excluded.line_count,
-        last_modified = excluded.last_modified,
-        indexed_at = unixepoch()
-      RETURNING id
-    `);
-
-    const result = stmt.get(path, contentHash, preview, language, sizeBytes, lineCount, lastModified) as { id: number };
-    return result.id;
-  }
-
-  getFile(path: string): FileMetadata | null {
-    const stmt = this.db.prepare(`
-      SELECT id, path, content_hash as contentHash, preview, language,
-             size_bytes as sizeBytes, last_modified as lastModified, indexed_at as indexedAt
-      FROM files WHERE path = ?
-    `);
-    return stmt.get(path) as FileMetadata | null;
-  }
-
-  getFileById(id: number): FileMetadata | null {
-    const stmt = this.db.prepare(`
-      SELECT id, path, content_hash as contentHash, preview, language,
-             size_bytes as sizeBytes, last_modified as lastModified, indexed_at as indexedAt
-      FROM files WHERE id = ?
-    `);
-    return stmt.get(id) as FileMetadata | null;
-  }
-
-  deleteFile(path: string): void {
-    const stmt = this.db.prepare('DELETE FROM files WHERE path = ?');
-    stmt.run(path);
-  }
-
-  getAllFiles(): FileMetadata[] {
-    const stmt = this.db.prepare(`
-      SELECT id, path, content_hash as contentHash, preview, language,
-             size_bytes as sizeBytes, last_modified as lastModified, indexed_at as indexedAt
-      FROM files ORDER BY path
-    `);
-    return stmt.all() as FileMetadata[];
-  }
-
-  getFileCount(): number {
-    const stmt = this.db.prepare('SELECT COUNT(*) as count FROM files');
-    const result = stmt.get() as { count: number };
-    return result.count;
-  }
-
-  getTotalLines(): number {
-    const stmt = this.db.prepare('SELECT COALESCE(SUM(line_count), 0) as total FROM files');
-    const result = stmt.get() as { total: number };
-    return result.total;
-  }
-
-  getLanguages(): string[] {
-    const stmt = this.db.prepare('SELECT DISTINCT language FROM files WHERE language IS NOT NULL ORDER BY language');
-    const results = stmt.all() as { language: string }[];
-    return results.map(r => r.language);
-  }
-
-  // Embedding operations
-  upsertEmbedding(fileId: number, embedding: Float32Array): void {
-    const buffer = Buffer.from(embedding.buffer);
-    const stmt = this.db.prepare(`
-      INSERT INTO embeddings (file_id, embedding, dimension)
-      VALUES (?, ?, ?)
-      ON CONFLICT(file_id) DO UPDATE SET
-        embedding = excluded.embedding,
-        dimension = excluded.dimension
-    `);
-    stmt.run(fileId, buffer, embedding.length);
-  }
-
-  getEmbedding(fileId: number): Float32Array | null {
-    const stmt = this.db.prepare('SELECT embedding, dimension FROM embeddings WHERE file_id = ?');
-    const result = stmt.get(fileId) as { embedding: Buffer; dimension: number } | undefined;
-
-    if (!result) return null;
-
-    return new Float32Array(result.embedding.buffer, result.embedding.byteOffset, result.dimension);
-  }
-
-  getAllEmbeddings(): Array<{ fileId: number; embedding: Float32Array }> {
-    const stmt = this.db.prepare('SELECT file_id, embedding, dimension FROM embeddings');
-    const results = stmt.all() as Array<{ file_id: number; embedding: Buffer; dimension: number }>;
-
-    return results.map(r => ({
-      fileId: r.file_id,
-      embedding: new Float32Array(r.embedding.buffer, r.embedding.byteOffset, r.dimension)
-    }));
-  }
-
-  // Search using cosine similarity (computed in JS since sqlite-vec may not be available)
-  search(queryEmbedding: Float32Array, limit: number = 10): SearchResult[] {
-    const allEmbeddings = this.getAllEmbeddings();
-    const results: Array<{ fileId: number; similarity: number }> = [];
-
-    for (const { fileId, embedding } of allEmbeddings) {
-      const similarity = this.cosineSimilarity(queryEmbedding, embedding);
-      results.push({ fileId, similarity });
-    }
-
-    // Sort by similarity descending
-    results.sort((a, b) => b.similarity - a.similarity);
-
-    // Get top results with file metadata
-    const topResults = results.slice(0, limit);
-    const searchResults: SearchResult[] = [];
-
-    for (const { fileId, similarity } of topResults) {
-      const file = this.getFileById(fileId);
-      if (file) {
-        searchResults.push({
-          file: file.path,
-          preview: file.preview,
-          similarity,
-          lineStart: 1,
-          lineEnd: 50, // Default, could be improved
-          lastModified: file.lastModified
-        });
-      }
-    }
-
-    return searchResults;
-  }
-
-  private cosineSimilarity(a: Float32Array, b: Float32Array): number {
-    if (a.length !== b.length) return 0;
-
-    let dotProduct = 0;
-    let normA = 0;
-    let normB = 0;
-
-    for (let i = 0; i < a.length; i++) {
-      dotProduct += a[i]! * b[i]!;
-      normA += a[i]! * a[i]!;
-      normB += b[i]! * b[i]!;
-    }
-
-    const magnitude = Math.sqrt(normA) * Math.sqrt(normB);
-    return magnitude === 0 ? 0 : dotProduct / magnitude;
-  }
-
-  // Decision operations
-  upsertDecision(decision: Decision, embedding?: Float32Array): void {
-    const embeddingBuffer = embedding ? Buffer.from(embedding.buffer) : null;
-    const stmt = this.db.prepare(`
-      INSERT INTO decisions (id, title, description, files, tags, created_at, embedding, author, status, superseded_by)
-      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
-      ON CONFLICT(id) DO UPDATE SET
-        title = excluded.title,
-        description = excluded.description,
-        files = excluded.files,
-        tags = excluded.tags,
-        embedding = excluded.embedding,
-        author = excluded.author,
-        status = excluded.status,
-        superseded_by = excluded.superseded_by
-    `);
-    stmt.run(
-      decision.id,
-      decision.title,
-      decision.description,
-      JSON.stringify(decision.files),
-      JSON.stringify(decision.tags),
-      Math.floor(decision.createdAt.getTime() / 1000),
-      embeddingBuffer,
-      decision.author || null,
-      decision.status || 'accepted',
-      decision.supersededBy || null
-    );
-  }
-
-  getDecision(id: string): Decision | null {
-    const stmt = this.db.prepare('SELECT * FROM decisions WHERE id = ?');
-    const row = stmt.get(id) as {
-      id: string;
-      title: string;
-      description: string;
-      files: string;
-      tags: string;
-      created_at: number;
-      author: string | null;
-      status: string | null;
-      superseded_by: string | null;
-    } | undefined;
-
-    if (!row) return null;
-
-    return {
-      id: row.id,
-      title: row.title,
-      description: row.description,
-      files: JSON.parse(row.files || '[]'),
-      tags: JSON.parse(row.tags || '[]'),
-      createdAt: new Date(row.created_at * 1000),
-      author: row.author || undefined,
-      status: (row.status as Decision['status']) || undefined,
-      supersededBy: row.superseded_by || undefined
-    };
-  }
-
-  getRecentDecisions(limit: number = 10): Decision[] {
-    const stmt = this.db.prepare(`
-      SELECT id, title, description, files, tags, created_at, author, status, superseded_by
-      FROM decisions
-      ORDER BY created_at DESC
-      LIMIT ?
-    `);
-    const rows = stmt.all(limit) as Array<{
-      id: string;
-      title: string;
-      description: string;
-      files: string;
-      tags: string;
-      created_at: number;
-      author: string | null;
-      status: string | null;
-      superseded_by: string | null;
-    }>;
-
-    return rows.map(row => ({
-      id: row.id,
-      title: row.title,
-      description: row.description,
-      files: JSON.parse(row.files || '[]'),
-      tags: JSON.parse(row.tags || '[]'),
-      createdAt: new Date(row.created_at * 1000),
-      author: row.author || undefined,
-      status: (row.status as Decision['status']) || undefined,
-      supersededBy: row.superseded_by || undefined
-    }));
-  }
-
-  // Phase 4: Get all decisions (for export)
-  getAllDecisions(): Decision[] {
-    const stmt = this.db.prepare(`
-      SELECT id, title, description, files, tags, created_at, author, status, superseded_by
-      FROM decisions
-      ORDER BY created_at ASC
-    `);
-    const rows = stmt.all() as Array<{
-      id: string;
-      title: string;
-      description: string;
-      files: string;
-      tags: string;
-      created_at: number;
-      author: string | null;
-      status: string | null;
-      superseded_by: string | null;
-    }>;
-
-    return rows.map(row => ({
-      id: row.id,
-      title: row.title,
-      description: row.description,
-      files: JSON.parse(row.files || '[]'),
-      tags: JSON.parse(row.tags || '[]'),
-      createdAt: new Date(row.created_at * 1000),
-      author: row.author || undefined,
-      status: (row.status as Decision['status']) || undefined,
-      supersededBy: row.superseded_by || undefined
-    }));
-  }
-
-  // Phase 4: Update decision status
-  updateDecisionStatus(
-    decisionId: string,
-    status: 'proposed' | 'accepted' | 'deprecated' | 'superseded',
-    supersededBy?: string
-  ): boolean {
-    const stmt = this.db.prepare(`
-      UPDATE decisions
-      SET status = ?, superseded_by = ?
-      WHERE id = ?
-    `);
-    const result = stmt.run(status, supersededBy || null, decisionId);
-    return result.changes > 0;
-  }
-
-  searchDecisions(queryEmbedding: Float32Array, limit: number = 5): Decision[] {
-    // Get all decisions with embeddings
-    const stmt = this.db.prepare(`
-      SELECT id, title, description, files, tags, created_at, embedding, author, status, superseded_by
-      FROM decisions
-      WHERE embedding IS NOT NULL
-    `);
-    const rows = stmt.all() as Array<{
-      id: string;
-      title: string;
-      description: string;
-      files: string;
-      tags: string;
-      created_at: number;
-      embedding: Buffer;
-      author: string | null;
-      status: string | null;
-      superseded_by: string | null;
-    }>;
-
-    if (rows.length === 0) {
-      return this.getRecentDecisions(limit);
-    }
-
-    // Calculate similarity for each
-    const results = rows.map(row => {
-      const embedding = new Float32Array(row.embedding.buffer, row.embedding.byteOffset, 384);
-      const similarity = this.cosineSimilarity(queryEmbedding, embedding);
-      return { row, similarity };
-    });
-
-    // Sort by similarity and return top results
-    results.sort((a, b) => b.similarity - a.similarity);
-
-    return results.slice(0, limit).map(({ row }) => ({
-      id: row.id,
-      title: row.title,
-      description: row.description,
-      files: JSON.parse(row.files || '[]'),
-      tags: JSON.parse(row.tags || '[]'),
-      createdAt: new Date(row.created_at * 1000),
-      author: row.author || undefined,
-      status: (row.status as Decision['status']) || undefined,
-      supersededBy: row.superseded_by || undefined
-    }));
-  }
-
-  // Dependency operations
-  addDependency(sourceFileId: number, targetFileId: number, relationship: string): void {
-    const stmt = this.db.prepare(`
-      INSERT OR IGNORE INTO dependencies (source_file_id, target_file_id, relationship)
-      VALUES (?, ?, ?)
-    `);
-    stmt.run(sourceFileId, targetFileId, relationship);
-  }
-
-  getDependencies(fileId: number): DependencyRelation[] {
-    const stmt = this.db.prepare(`
-      SELECT source_file_id as sourceFileId, target_file_id as targetFileId, relationship
-      FROM dependencies
-      WHERE source_file_id = ?
-    `);
-    return stmt.all(fileId) as DependencyRelation[];
-  }
-
-  getDependents(fileId: number): DependencyRelation[] {
-    const stmt = this.db.prepare(`
-      SELECT source_file_id as sourceFileId, target_file_id as targetFileId, relationship
-      FROM dependencies
-      WHERE target_file_id = ?
-    `);
-    return stmt.all(fileId) as DependencyRelation[];
-  }
-
-  clearDependencies(fileId: number): void {
-    const stmt = this.db.prepare('DELETE FROM dependencies WHERE source_file_id = ?');
-    stmt.run(fileId);
-  }
-
-  // Project summary
-  updateProjectSummary(
-    name: string,
-    description: string,
-    languages: string[],
-    keyDirectories: string[],
-    architectureNotes: string
-  ): void {
-    const stmt = this.db.prepare(`
-      INSERT INTO project_summary (id, name, description, languages, key_directories, architecture_notes, updated_at)
-      VALUES (1, ?, ?, ?, ?, ?, unixepoch())
-      ON CONFLICT(id) DO UPDATE SET
-        name = excluded.name,
-        description = excluded.description,
-        languages = excluded.languages,
-        key_directories = excluded.key_directories,
-        architecture_notes = excluded.architecture_notes,
-        updated_at = unixepoch()
-    `);
-    stmt.run(name, description, JSON.stringify(languages), JSON.stringify(keyDirectories), architectureNotes);
-  }
-
-  getProjectSummary(): { name: string; description: string; languages: string[]; keyDirectories: string[]; architectureNotes: string } | null {
-    const stmt = this.db.prepare('SELECT name, description, languages, key_directories, architecture_notes FROM project_summary WHERE id = 1');
-    const row = stmt.get() as {
-      name: string;
-      description: string;
-      languages: string;
-      key_directories: string;
-      architecture_notes: string;
-    } | undefined;
-
-    if (!row) return null;
-
-    return {
-      name: row.name,
-      description: row.description,
-      languages: JSON.parse(row.languages || '[]'),
-      keyDirectories: JSON.parse(row.key_directories || '[]'),
-      architectureNotes: row.architecture_notes
-    };
-  }
-
-  // Phase 2: Symbol operations
-
-  clearSymbols(fileId: number): void {
-    this.db.prepare('DELETE FROM symbols WHERE file_id = ?').run(fileId);
-  }
-
-  insertSymbol(symbol: CodeSymbol): number {
-    const stmt = this.db.prepare(`
-      INSERT INTO symbols (file_id, kind, name, signature, docstring, line_start, line_end, exported)
-      VALUES (?, ?, ?, ?, ?, ?, ?, ?)
-    `);
-    const result = stmt.run(
-      symbol.fileId,
-      symbol.kind,
-      symbol.name,
-      symbol.signature || null,
-      symbol.docstring || null,
-      symbol.lineStart,
-      symbol.lineEnd,
-      symbol.exported ? 1 : 0
-    );
-    return Number(result.lastInsertRowid);
-  }
-
-  insertSymbols(symbols: CodeSymbol[]): void {
-    const stmt = this.db.prepare(`
-      INSERT INTO symbols (file_id, kind, name, signature, docstring, line_start, line_end, exported)
-      VALUES (?, ?, ?, ?, ?, ?, ?, ?)
-    `);
-
-    const insertMany = this.db.transaction((syms: CodeSymbol[]) => {
-      for (const s of syms) {
-        stmt.run(s.fileId, s.kind, s.name, s.signature || null, s.docstring || null, s.lineStart, s.lineEnd, s.exported ? 1 : 0);
-      }
-    });
-
-    insertMany(symbols);
-  }
-
-  getSymbolsByFile(fileId: number): CodeSymbol[] {
-    const stmt = this.db.prepare(`
-      SELECT s.id, s.file_id as fileId, f.path as filePath, s.kind, s.name, s.signature, s.docstring,
-             s.line_start as lineStart, s.line_end as lineEnd, s.exported
-      FROM symbols s
-      JOIN files f ON s.file_id = f.id
-      WHERE s.file_id = ?
-      ORDER BY s.line_start
-    `);
-    const rows = stmt.all(fileId) as Array<{
-      id: number;
-      fileId: number;
-      filePath: string;
-      kind: string;
-      name: string;
-      signature: string | null;
-      docstring: string | null;
-      lineStart: number;
-      lineEnd: number;
-      exported: number;
-    }>;
-
-    return rows.map(r => ({
-      id: r.id,
-      fileId: r.fileId,
-      filePath: r.filePath,
-      kind: r.kind as SymbolKind,
-      name: r.name,
-      signature: r.signature || undefined,
-      docstring: r.docstring || undefined,
-      lineStart: r.lineStart,
-      lineEnd: r.lineEnd,
-      exported: r.exported === 1
-    }));
-  }
-
-  searchSymbols(name: string, kind?: SymbolKind, limit: number = 20): CodeSymbol[] {
-    let query = `
-      SELECT s.id, s.file_id as fileId, f.path as filePath, s.kind, s.name, s.signature, s.docstring,
-             s.line_start as lineStart, s.line_end as lineEnd, s.exported
-      FROM symbols s
-      JOIN files f ON s.file_id = f.id
-      WHERE s.name LIKE ?
-    `;
-
-    const params: (string | number)[] = [`%${name}%`];
-
-    if (kind) {
-      query += ' AND s.kind = ?';
-      params.push(kind);
-    }
-
-    query += ' ORDER BY CASE WHEN s.name = ? THEN 0 WHEN s.name LIKE ? THEN 1 ELSE 2 END, s.name LIMIT ?';
-    params.push(name, `${name}%`, limit);
-
-    const stmt = this.db.prepare(query);
-    const rows = stmt.all(...params) as Array<{
-      id: number;
-      fileId: number;
-      filePath: string;
-      kind: string;
-      name: string;
-      signature: string | null;
-      docstring: string | null;
-      lineStart: number;
-      lineEnd: number;
-      exported: number;
-    }>;
-
-    return rows.map(r => ({
-      id: r.id,
-      fileId: r.fileId,
-      filePath: r.filePath,
-      kind: r.kind as SymbolKind,
-      name: r.name,
-      signature: r.signature || undefined,
-      docstring: r.docstring || undefined,
-      lineStart: r.lineStart,
-      lineEnd: r.lineEnd,
-      exported: r.exported === 1
-    }));
-  }
-
-  getSymbolByName(name: string, kind?: SymbolKind): CodeSymbol | null {
-    let query = `
-      SELECT s.id, s.file_id as fileId, f.path as filePath, s.kind, s.name, s.signature, s.docstring,
-             s.line_start as lineStart, s.line_end as lineEnd, s.exported
-      FROM symbols s
-      JOIN files f ON s.file_id = f.id
-      WHERE s.name = ?
-    `;
-
-    const params: string[] = [name];
-
-    if (kind) {
-      query += ' AND s.kind = ?';
-      params.push(kind);
-    }
-
-    query += ' LIMIT 1';
-
-    const stmt = this.db.prepare(query);
-    const row = stmt.get(...params) as {
-      id: number;
-      fileId: number;
-      filePath: string;
-      kind: string;
-      name: string;
-      signature: string | null;
-      docstring: string | null;
-      lineStart: number;
-      lineEnd: number;
-      exported: number;
-    } | undefined;
-
-    if (!row) return null;
-
-    return {
-      id: row.id,
-      fileId: row.fileId,
-      filePath: row.filePath,
-      kind: row.kind as SymbolKind,
-      name: row.name,
-      signature: row.signature || undefined,
-      docstring: row.docstring || undefined,
-      lineStart: row.lineStart,
-      lineEnd: row.lineEnd,
-      exported: row.exported === 1
-    };
-  }
-
-  getSymbolCount(): number {
-    const stmt = this.db.prepare('SELECT COUNT(*) as count FROM symbols');
-    const result = stmt.get() as { count: number };
-    return result.count;
-  }
-
-  // Phase 2: Import operations
-
-  clearImports(fileId: number): void {
-    this.db.prepare('DELETE FROM imports WHERE file_id = ?').run(fileId);
-  }
-
-  insertImports(imports: Import[]): void {
-    const stmt = this.db.prepare(`
-      INSERT INTO imports (file_id, imported_from, imported_symbols, is_default, is_namespace, line_number)
-      VALUES (?, ?, ?, ?, ?, ?)
-    `);
-
-    const insertMany = this.db.transaction((imps: Import[]) => {
-      for (const i of imps) {
-        stmt.run(
-          i.fileId,
-          i.importedFrom,
-          JSON.stringify(i.importedSymbols),
-          i.isDefault ? 1 : 0,
-          i.isNamespace ? 1 : 0,
-          i.lineNumber
-        );
-      }
-    });
-
-    insertMany(imports);
-  }
-
-  getImportsByFile(fileId: number): Import[] {
-    const stmt = this.db.prepare(`
-      SELECT i.file_id as fileId, f.path as filePath, i.imported_from as importedFrom,
-             i.imported_symbols as importedSymbols, i.is_default as isDefault,
-             i.is_namespace as isNamespace, i.line_number as lineNumber
-      FROM imports i
-      JOIN files f ON i.file_id = f.id
-      WHERE i.file_id = ?
-    `);
-    const rows = stmt.all(fileId) as Array<{
-      fileId: number;
-      filePath: string;
-      importedFrom: string;
-      importedSymbols: string;
-      isDefault: number;
-      isNamespace: number;
-      lineNumber: number;
-    }>;
-
-    return rows.map(r => ({
-      fileId: r.fileId,
-      filePath: r.filePath,
-      importedFrom: r.importedFrom,
-      importedSymbols: JSON.parse(r.importedSymbols),
-      isDefault: r.isDefault === 1,
-      isNamespace: r.isNamespace === 1,
-      lineNumber: r.lineNumber
-    }));
-  }
-
-  getFilesImporting(modulePath: string): Array<{ fileId: number; filePath: string }> {
-    // Use exact matching with common import path patterns to avoid false positives
-    // e.g., "user" should not match "super-user-service"
-    const stmt = this.db.prepare(`
-      SELECT DISTINCT i.file_id as fileId, f.path as filePath
-      FROM imports i
-      JOIN files f ON i.file_id = f.id
-      WHERE i.imported_from = ?
-         OR i.imported_from LIKE ?
-         OR i.imported_from LIKE ?
-         OR i.imported_from LIKE ?
-    `);
-    return stmt.all(
-      modulePath,
-      `%/${modulePath}`,      // ends with /modulePath
-      `./${modulePath}`,      // relative ./modulePath
-      `../${modulePath}`      // parent ../modulePath
-    ) as Array<{ fileId: number; filePath: string }>;
-  }
-
-  // Phase 2: Export operations
-
-  clearExports(fileId: number): void {
-    this.db.prepare('DELETE FROM exports WHERE file_id = ?').run(fileId);
-  }
-
-  insertExports(exports: Export[]): void {
-    const stmt = this.db.prepare(`
-      INSERT INTO exports (file_id, exported_name, local_name, is_default, line_number)
-      VALUES (?, ?, ?, ?, ?)
-    `);
-
-    const insertMany = this.db.transaction((exps: Export[]) => {
-      for (const e of exps) {
-        stmt.run(e.fileId, e.exportedName, e.localName || null, e.isDefault ? 1 : 0, e.lineNumber);
-      }
-    });
-
-    insertMany(exports);
-  }
-
-  getExportsByFile(fileId: number): Export[] {
-    const stmt = this.db.prepare(`
-      SELECT e.file_id as fileId, f.path as filePath, e.exported_name as exportedName,
-             e.local_name as localName, e.is_default as isDefault, e.line_number as lineNumber
-      FROM exports e
-      JOIN files f ON e.file_id = f.id
-      WHERE e.file_id = ?
-    `);
-    const rows = stmt.all(fileId) as Array<{
-      fileId: number;
-      filePath: string;
-      exportedName: string;
-      localName: string | null;
-      isDefault: number;
-      lineNumber: number;
-    }>;
-
-    return rows.map(r => ({
-      fileId: r.fileId,
-      filePath: r.filePath,
-      exportedName: r.exportedName,
-      localName: r.localName || undefined,
-      isDefault: r.isDefault === 1,
-      lineNumber: r.lineNumber
-    }));
-  }
-
-  // Phase 2: Dependency graph helpers
-
-  getFileDependencies(filePath: string): Array<{ file: string; imports: string[] }> {
-    const file = this.getFile(filePath);
-    if (!file) return [];
-
-    const imports = this.getImportsByFile(file.id);
-    const deps: Array<{ file: string; imports: string[] }> = [];
-
-    for (const imp of imports) {
-      deps.push({
-        file: imp.importedFrom,
-        imports: imp.importedSymbols
-      });
-    }
-
-    return deps;
-  }
-
-  getFileDependents(filePath: string): Array<{ file: string; imports: string[] }> {
-    // Find files that import this file
-    const fileName = filePath.split(/[/\\]/).pop()?.replace(/\.[^.]+$/, '') || '';
-    const importers = this.getFilesImporting(fileName);
-
-    const deps: Array<{ file: string; imports: string[] }> = [];
-
-    for (const importer of importers) {
-      const imports = this.getImportsByFile(importer.fileId);
-      const relevantImport = imports.find(i => {
-        const importedName = i.importedFrom.split(/[/\\]/).pop()?.replace(/\.[^.]+$/, '') || '';
-        return importedName === fileName || i.importedFrom.endsWith(`/${fileName}`) || i.importedFrom.endsWith(`./${fileName}`);
-      });
-      if (relevantImport) {
-        deps.push({
-          file: importer.filePath,
-          imports: relevantImport.importedSymbols
-        });
-      }
-    }
-
-    return deps;
-  }
-
-  /**
-   * Get ALL files affected by a change, walking the dependency graph.
-   * depth=1 is direct importers only. depth=3 catches ripple effects.
-   */
-  getTransitiveDependents(
-    filePath: string,
-    maxDepth: number = 3
-  ): Array<{ file: string; depth: number; imports: string[] }> {
-    const visited = new Map<string, { depth: number; imports: string[] }>();
-    const queue: Array<{ path: string; depth: number }> = [{ path: filePath, depth: 0 }];
-
-    while (queue.length > 0) {
-      const current = queue.shift()!;
-      if (current.depth >= maxDepth) continue;
-      if (visited.has(current.path) && visited.get(current.path)!.depth <= current.depth) continue;
-
-      const dependents = this.getFileDependents(current.path);
-      for (const dep of dependents) {
-        const existingDepth = visited.get(dep.file)?.depth ?? Infinity;
-        const newDepth = current.depth + 1;
-
-        if (newDepth < existingDepth) {
-          visited.set(dep.file, { depth: newDepth, imports: dep.imports });
-          queue.push({ path: dep.file, depth: newDepth });
-        }
-      }
-    }
-
-    visited.delete(filePath); // don't include the original file
-    return Array.from(visited.entries())
-      .map(([file, info]) => ({ file, ...info }))
-      .sort((a, b) => a.depth - b.depth);
-  }
-
-  /**
-   * Get the full import graph as an adjacency list.
-   * Returns { file → [files it imports] } for the whole project.
-   */
-  getFullDependencyGraph(): Map<string, string[]> {
-    const stmt = this.db.prepare(`
-      SELECT f.path as filePath, i.imported_from as importedFrom
-      FROM imports i
-      JOIN files f ON i.file_id = f.id
-    `);
-    const rows = stmt.all() as Array<{ filePath: string; importedFrom: string }>;
-
-    const graph = new Map<string, string[]>();
-    for (const row of rows) {
-      if (!graph.has(row.filePath)) graph.set(row.filePath, []);
-      graph.get(row.filePath)!.push(row.importedFrom);
-    }
-    return graph;
-  }
-
-  /**
-   * Find circular dependencies in the project.
-   * Returns arrays of file paths that form cycles.
-   */
-  findCircularDependencies(): Array<string[]> {
-    const graph = this.getFullDependencyGraph();
-    const cycles: Array<string[]> = [];
-    const visited = new Set<string>();
-    const stack = new Set<string>();
-
-    const dfs = (node: string, path: string[]) => {
-      if (stack.has(node)) {
-        // Found cycle
-        const cycleStart = path.indexOf(node);
-        if (cycleStart >= 0) {
-          cycles.push(path.slice(cycleStart).concat(node));
-        }
-        return;
-      }
-      if (visited.has(node)) return;
-
-      visited.add(node);
-      stack.add(node);
-      path.push(node);
-
-      const deps = graph.get(node) || [];
-      for (const dep of deps) {
-        // Resolve relative imports to file paths
-        const resolved = this.resolveImportPath(node, dep);
-        if (resolved) dfs(resolved, [...path]);
-      }
-
-      stack.delete(node);
-    };
-
-    for (const file of graph.keys()) {
-      dfs(file, []);
-    }
-
-    // Deduplicate cycles (same cycle can be found from different starting points)
-    const uniqueCycles: Array<string[]> = [];
-    const seen = new Set<string>();
-    for (const cycle of cycles) {
-      const normalized = [...cycle].sort().join('|');
-      if (!seen.has(normalized)) {
-        seen.add(normalized);
-        uniqueCycles.push(cycle);
-      }
-    }
-
-    return uniqueCycles;
-  }
-
-  /**
-   * Resolve a relative import path to an actual file path in the database.
-   */
-  resolveImportPath(fromFile: string, importPath: string): string | null {
-    // Skip external packages (node_modules)
-    if (!importPath.startsWith('.') && !importPath.startsWith('/')) return null;
-
-    const dir = fromFile.split(/[/\\]/).slice(0, -1).join('/');
-
-    // Normalize the import path
-    let resolved = importPath;
-    if (importPath.startsWith('./')) {
-      resolved = dir + '/' + importPath.slice(2);
-    } else if (importPath.startsWith('../')) {
-      const parts = dir.split('/');
-      let impParts = importPath.split('/');
-      while (impParts[0] === '..') {
-        parts.pop();
-        impParts.shift();
-      }
-      resolved = parts.join('/') + '/' + impParts.join('/');
-    }
-
-    // Remove extension if present
-    const baseName = resolved.replace(/\.(ts|tsx|js|jsx|mjs|cjs)$/, '');
-
-    // Try to find a matching file in the database
-    const stmt = this.db.prepare(`
-      SELECT path FROM files
-      WHERE path = ? OR path = ? OR path = ? OR path = ?
-         OR path = ? OR path = ?
-      LIMIT 1
-    `);
-    const result = stmt.get(
-      `${baseName}.ts`, `${baseName}.tsx`,
-      `${baseName}.js`, `${baseName}.jsx`,
-      `${baseName}/index.ts`, `${baseName}/index.js`
-    ) as { path: string } | undefined;
-
-    return result?.path || null;
-  }
-
-  /**
-   * Resolve an import path to a file record in the database.
-   * Used by indexer to build the dependencies table.
-   */
-  resolveImportToFile(
-    sourceFilePath: string,
-    importPath: string
-  ): { id: number; path: string } | null {
-    // Skip external packages
-    if (!importPath.startsWith('.') && !importPath.startsWith('/')) return null;
-
-    const sourceDir = sourceFilePath.split(/[/\\]/).slice(0, -1).join('/');
-
-    // Normalize the import path
-    let resolved = importPath;
-    if (importPath.startsWith('./')) {
-      resolved = sourceDir + '/' + importPath.slice(2);
-    } else if (importPath.startsWith('../')) {
-      const parts = sourceDir.split('/');
-      let impParts = importPath.split('/');
-      while (impParts[0] === '..') {
-        parts.pop();
-        impParts.shift();
-      }
-      resolved = parts.join('/') + '/' + impParts.join('/');
-    }
-
-    // Remove extension if present
-    resolved = resolved.replace(/\.(ts|tsx|js|jsx|mjs|cjs)$/, '');
-
-    // Try exact matches with common extensions
-    const stmt = this.db.prepare(`
-      SELECT id, path FROM files
-      WHERE path = ? OR path = ? OR path = ? OR path = ?
-         OR path = ? OR path = ?
-      LIMIT 1
-    `);
-
-    const result = stmt.get(
-      `${resolved}.ts`, `${resolved}.tsx`,
-      `${resolved}.js`, `${resolved}.jsx`,
-      `${resolved}/index.ts`, `${resolved}/index.js`
-    ) as { id: number; path: string } | undefined;
-
-    return result || null;
-  }
-}