scip-query 0.1.0

package/dist/cli.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli.ts","../src/db.ts","../src/gitignore-filter.ts","../src/config.ts","../src/reindex/index.ts","../src/reindex/detect.ts","../src/reindex/indexers.ts","../src/reindex/install.ts","../src/watch.ts","../src/queries/stats.ts","../src/queries/files.ts","../src/symbol-parser.ts","../src/queries/clean-signature.ts","../src/queries/symbols.ts","../src/queries/methods.ts","../src/queries/refs.ts","../src/queries/trace.ts","../src/queries/deps.ts","../src/queries/system.ts","../src/queries/surface.ts","../src/query-support.ts","../src/queries/dead.ts","../src/queries/hotspots.ts","../src/queries/imports.ts","../src/queries/outline.ts","../src/queries/members.ts","../src/queries/fan.ts","../src/queries/coupling.ts","../src/queries/cycles.ts","../src/queries/bottlenecks.ts","../src/queries/isolated.ts","../src/queries/by-kind.ts","../src/queries/test-coverage.ts","../src/queries/doc-coverage.ts","../src/queries/deep-chains.ts","../src/queries/hierarchy.ts","../src/queries/call-graph.ts","../src/queries/similar.ts","../src/queries/similar-files.ts","../src/queries/similar-chains.ts","../src/queries/extract-candidates.ts","../src/queries/affected.ts","../src/queries/change-surface.ts","../src/queries/diff-impact.ts","../src/queries/drift.ts","../src/queries/wrapper-candidates.ts","../src/queries/passthrough-candidates.ts","../src/queries/stale-abstractions.ts","../src/queries/complexity-hotspots.ts","../src/queries/health.ts","../src/queries/convergence.ts","../src/queries/code.ts","../src/queries/complexity.ts","../src/queries/dataflow.ts","../src/queries/slice.ts","../src/queries/redundant-reexports.ts","../src/queries/similar-signatures.ts","../src/setup.ts"],"sourcesContent":["import { program } from 'commander';\nimport { existsSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { ScipDatabase } from './db.js';\nimport { createGitignoreFilter } from './gitignore-filter.js';\nimport { loadProjectConfig, resolveIndexPaths, initProjectConfig } from './config.js';\nimport { reindex, detectLanguages } from './reindex/index.js';\nimport { Watcher } from './watch.js';\nimport * as queries from './queries/index.js';\nimport type { ScipQueryConfig, DeadOptions, WatcherStatus } from './types.js';\nimport { installSkills, isScipInstalled, printScipInstallInstructions } from './setup.js';\n\n// ── Helpers ────────────────────────────────────────────────\n\nfunction resolveProjectRoot(): string {\n  return process.env['SCIP_QUERY_PROJECT_ROOT'] ?? process.cwd();\n}\n\nfunction openDb(): ScipDatabase {\n  const projectRoot = resolveProjectRoot();\n  const config = loadProjectConfig(projectRoot);\n  const paths = resolveIndexPaths(projectRoot, config);\n\n  // Also check legacy location (project root) for backwards compat\n  const dbPath = process.env['SCIP_QUERY_INDEX_DB']\n    ?? (existsSync(paths.dbPath) ? paths.dbPath : join(projectRoot, 'index.db'));\n\n  if (!existsSync(dbPath)) {\n    console.error(`error: No index.db found. Run: scip-query reindex`);\n    process.exit(1);\n  }\n\n  const dbConfig: ScipQueryConfig = {\n    dbPath,\n    indexPath: process.env['SCIP_QUERY_INDEX_SCIP'] ?? paths.indexPath,\n    projectRoot,\n  };\n\n  const filter = createGitignoreFilter(projectRoot);\n  return new ScipDatabase(dbConfig, filter);\n}\n\nfunction withDb(run: (db: ScipDatabase) => void): void {\n  const db = openDb();\n  try {\n    run(db);\n  } finally {\n    db.close();\n  }\n}\n\nfunction runQuery<T>(\n  query: (db: ScipDatabase) => T,\n  render: (result: T) => void,\n): void {\n  withDb((db) => {\n    render(query(db));\n  });\n}\n\n// ── CLI Definition ─────────────────────────────────────────\n\nprogram\n  .name('scip-query')\n  .description('Language-agnostic code intelligence CLI powered by SCIP indexes')\n  .version('0.1.0');\n\n// reindex\nprogram\n  .command('reindex')\n  .description('Index the codebase and convert to SQLite')\n  .option('-l, --language <lang>', 'Index only this language (can be repeated)', collect, [])\n  .option('--pnpm-workspaces', 'Enable pnpm workspace support (TypeScript)')\n  .action(async (opts) => {\n    const projectRoot = resolveProjectRoot();\n    try {\n      const result = await reindex({\n        projectRoot,\n        languages: opts.language.length > 0 ? opts.language : undefined,\n        pnpmWorkspaces: opts.pnpmWorkspaces,\n      });\n      console.log(`Indexed ${result.languages.join(', ')} in ${(result.durationMs / 1000).toFixed(1)}s`);\n    } catch (err) {\n      console.error(`error: ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\n// stats\nprogram\n  .command('stats')\n  .description('Show index statistics')\n  .action(() => {\n    runQuery(\n      (db) => queries.stats(db),\n      (s) => {\n        console.log(`Documents:   ${s.documents}`);\n        console.log(`Symbols:     ${s.symbols}`);\n        console.log(`Definitions: ${s.definitions}`);\n        console.log(`References:  ${s.references}`);\n        console.log(`Index size:  ${formatBytes(s.indexSizeBytes)}`);\n        if (s.lastBuilt) {\n          console.log(`Last built:  ${s.lastBuilt.toISOString().replace('T', ' ').slice(0, 19)}`);\n        }\n      },\n    );\n  });\n\n// files\nprogram\n  .command('files <pattern>')\n  .description('Find files matching a pattern')\n  .action((pattern) => {\n    runQuery(\n      (db) => queries.files(db, pattern),\n      (results) => {\n        for (const r of results) console.log(r.relativePath);\n      },\n    );\n  });\n\n// symbols\nprogram\n  .command('symbols <file>')\n  .description('List symbols defined in a file (with line ranges + signatures)')\n  .action((file) => {\n    runQuery(\n      (db) => queries.symbols(db, file),\n      (results) => {\n        for (const r of results) {\n          const sig = r.signature ? `  — ${r.signature}` : '';\n          console.log(`  ${r.startLine}-${r.endLine}  ${r.shortName}${sig}`);\n        }\n      },\n    );\n  });\n\n// methods\nprogram\n  .command('methods <className>')\n  .description('List methods of a class (with line ranges)')\n  .action((className) => {\n    runQuery(\n      (db) => queries.methods(db, className),\n      (results) => {\n        for (const r of results) {\n          console.log(`  ${r.startLine}-${r.endLine}  ${r.name}`);\n        }\n      },\n    );\n  });\n\n// refs\nprogram\n  .command('refs <symbol>')\n  .description('Find all files referencing a symbol')\n  .action((symbol) => {\n    runQuery(\n      (db) => queries.refs(db, symbol),\n      (results) => {\n        let prevFile = '';\n        for (const r of results) {\n          if (r.relativePath !== prevFile) {\n            if (prevFile) console.log('');\n            console.log(r.relativePath);\n            prevFile = r.relativePath;\n          }\n          console.log(`  line ${r.line}`);\n        }\n      },\n    );\n  });\n\n// trace\nprogram\n  .command('trace <symbol>')\n  .description('Trace a symbol: definition + all references')\n  .action((symbol) => {\n    runQuery(\n      (db) => queries.trace(db, symbol),\n      (result) => {\n        console.log('═══ DEFINITION ═══');\n        for (const d of result.definitions) {\n          const sig = d.signature ? `  — ${d.signature}` : '';\n          console.log(`  ${d.relativePath}:${d.startLine}-${d.endLine}${sig}`);\n        }\n\n        console.log('\\n═══ REFERENCED BY ═══');\n        for (const ref of result.referencedBy) {\n          console.log(`  ${ref}`);\n        }\n      },\n    );\n  });\n\n// deps\nprogram\n  .command('deps <file>')\n  .description('Files this file depends on (internal)')\n  .action((file) => {\n    runQuery(\n      (db) => queries.deps(db, file),\n      (results) => {\n        for (const r of results) console.log(r.relativePath);\n      },\n    );\n  });\n\n// rdeps\nprogram\n  .command('rdeps <file>')\n  .description('Files that depend on this file/module')\n  .action((file) => {\n    runQuery(\n      (db) => queries.rdeps(db, file),\n      (results) => {\n        for (const r of results) console.log(r.relativePath);\n      },\n    );\n  });\n\n// system\nprogram\n  .command('system <module>')\n  .description('Full module map: files, symbols, deps in/out')\n  .action((module) => {\n    runQuery(\n      (db) => queries.system(db, module),\n      (result) => {\n        console.log('═══ FILES ═══');\n        for (const f of result.files) console.log(f);\n\n        console.log('\\n═══ EXPORTED SYMBOLS ═══');\n        for (const s of result.symbols) {\n          console.log(`  ${s.startLine}-${s.endLine}  ${s.shortName}`);\n        }\n\n        console.log('\\n═══ DEPENDS ON (internal) ═══');\n        for (const d of result.dependsOn) console.log(`  ${d}`);\n\n        console.log('\\n═══ DEPENDED ON BY ═══');\n        for (const d of result.dependedOnBy) console.log(`  ${d}`);\n      },\n    );\n  });\n\n// surface\nprogram\n  .command('surface <module>')\n  .description('What symbols consumers actually use from this module')\n  .action((module) => {\n    runQuery(\n      (db) => queries.surface(db, module),\n      (results) => {\n        for (const r of results) {\n          console.log(`  ${r.consumer} → ${r.shortName}`);\n        }\n      },\n    );\n  });\n\n// dead\nprogram\n  .command('dead [scope]')\n  .description('Find dead code and file-internal symbols (no cross-file consumers)')\n  .option('--min-loc <n>', 'Only show symbols >= N lines', parseIntSafe, 1)\n  .option('--include-tests', 'Include test files')\n  .option('--skip-barrels', 'Ignore refs from barrel re-export files')\n  .option('--include-members', 'Include class members')\n  .action((scope, opts) => {\n    withDb((db) => {\n      const deadOpts: DeadOptions = {\n        scope: scope || undefined,\n        minLoc: opts.minLoc,\n        includeTests: opts.includeTests,\n        skipBarrels: opts.skipBarrels,\n        includeMembers: opts.includeMembers,\n      };\n\n      const result = queries.dead(db, deadOpts);\n\n      if (result.symbols.length === 0) {\n        console.log('No dead code found.');\n        return;\n      }\n\n      let prevFile = '';\n      for (const s of result.symbols) {\n        if (s.relativePath !== prevFile) {\n          if (prevFile) console.log('');\n          console.log(s.relativePath);\n          prevFile = s.relativePath;\n        }\n        const tag = s.kind === 'dead-code' ? '[dead code]' : '[file-internal only]';\n        console.log(`  ${s.startLine}-${s.endLine}  (${s.loc} LOC)  ${s.shortName}  ${tag}`);\n      }\n\n      console.log('\\n───────────────────────────');\n      console.log(\n        `Total: ${result.totalCount} symbols (${result.deadCodeCount} dead code, ` +\n        `${result.fileInternalCount} file-internal), ${result.totalLoc} LOC`,\n      );\n    });\n  });\n\n// hotspots\nprogram\n  .command('hotspots')\n  .description('Most-referenced symbols in the codebase (choke points)')\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 30)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .action((opts) => {\n    runQuery(\n      (db) => queries.hotspots(db, { limit: opts.limit, scope: opts.scope }),\n      (results) => {\n        console.log('  refs  files  symbol');\n        console.log('  ────  ─────  ──────');\n        for (const r of results) {\n          console.log(`  ${String(r.refCount).padStart(4)}  ${String(r.fileCount).padStart(5)}  ${r.shortName}`);\n        }\n      },\n    );\n  });\n\n// imports\nprogram\n  .command('imports <file>')\n  .description('What symbols does this file import?')\n  .action((file) => {\n    runQuery(\n      (db) => queries.imports(db, file),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No imports found (indexer may not emit role=2 for this language).');\n        }\n        for (const r of results) {\n          console.log(`  ${r.shortName}  ← ${r.fromFile}`);\n        }\n      },\n    );\n  });\n\n// imported-by\nprogram\n  .command('imported-by <symbol>')\n  .description('Which files import this symbol?')\n  .action((symbol) => {\n    runQuery(\n      (db) => queries.importedBy(db, symbol),\n      (results) => {\n        for (const r of results) {\n          console.log(`  ${r.fromFile}`);\n        }\n      },\n    );\n  });\n\n// unused-imports\nprogram\n  .command('unused-imports <file>')\n  .description('Find imports not referenced in the same file')\n  .action((file) => {\n    runQuery(\n      (db) => queries.unusedImports(db, file),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No unused imports found.');\n        } else {\n          for (const r of results) {\n            console.log(`  ${r.shortName}  in ${r.importedIn}`);\n          }\n          console.log(`\\n${results.length} unused import(s)`);\n        }\n      },\n    );\n  });\n\n// outline\nprogram\n  .command('outline <file>')\n  .description('Tree view of symbols in a file (using nesting hierarchy)')\n  .action((file) => {\n    runQuery(\n      (db) => queries.outline(db, file),\n      (roots) => {\n        function printTree(nodes: typeof roots, indent: number): void {\n          for (const n of nodes) {\n            const prefix = '  '.repeat(indent);\n            console.log(`${prefix}${n.startLine}-${n.endLine}  ${n.shortName}`);\n            printTree(n.children, indent + 1);\n          }\n        }\n        printTree(roots, 0);\n      },\n    );\n  });\n\n// members\nprogram\n  .command('members <symbol>')\n  .description('All children of a symbol (methods, fields, nested types)')\n  .action((symbol) => {\n    runQuery(\n      (db) => queries.members(db, symbol),\n      (results) => {\n        for (const r of results) {\n          console.log(`  ${r.startLine}-${r.endLine}  [${r.kind}]  ${r.shortName}`);\n        }\n      },\n    );\n  });\n\n// fan-in\nprogram\n  .command('fan-in [symbol]')\n  .description('How many files reference a symbol (or top fan-in across codebase)')\n  .option('-n, --limit <n>', 'Number of results for top mode', parseIntSafe, 30)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .action((symbol, opts) => {\n    withDb((db) => {\n      if (symbol) {\n        const results = queries.fanIn(db, symbol);\n        for (const r of results) {\n          console.log(`  ${String(r.count).padStart(4)} files  ${r.name}`);\n        }\n      } else {\n        const results = queries.topFanIn(db, { limit: opts.limit, scope: opts.scope });\n        console.log('  files  symbol');\n        console.log('  ─────  ──────');\n        for (const r of results) {\n          console.log(`  ${String(r.count).padStart(5)}  ${r.name}`);\n        }\n      }\n    });\n  });\n\n// fan-out\nprogram\n  .command('fan-out [file]')\n  .description('How many external symbols a file uses (or top fan-out across codebase)')\n  .option('-n, --limit <n>', 'Number of results for top mode', parseIntSafe, 30)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .action((file, opts) => {\n    withDb((db) => {\n      if (file) {\n        const results = queries.fanOut(db, file);\n        for (const r of results) {\n          console.log(`  ${String(r.count).padStart(4)} symbols  ${r.name}`);\n        }\n      } else {\n        const results = queries.topFanOut(db, { limit: opts.limit, scope: opts.scope });\n        console.log('  symbols  file');\n        console.log('  ───────  ────');\n        for (const r of results) {\n          console.log(`  ${String(r.count).padStart(7)}  ${r.name}`);\n        }\n      }\n    });\n  });\n\n// coupling\nprogram\n  .command('coupling [file1] [file2]')\n  .description('Coupling between two files, or top coupled pairs in codebase')\n  .option('-n, --limit <n>', 'Number of results for top mode', parseIntSafe, 20)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .action((file1, file2, opts) => {\n    withDb((db) => {\n      if (file1 && file2) {\n        const result = queries.coupling(db, file1, file2);\n        console.log(`${result.file1} ↔ ${result.file2}: ${result.sharedSymbols} shared symbols`);\n      } else {\n        const results = queries.topCoupling(db, { limit: opts.limit, scope: opts.scope });\n        console.log('  shared  file1 → file2');\n        console.log('  ──────  ─────────────');\n        for (const r of results) {\n          console.log(`  ${String(r.sharedSymbols).padStart(6)}  ${r.file1} → ${r.file2}`);\n        }\n      }\n    });\n  });\n\n// cycles\nprogram\n  .command('cycles')\n  .description('Detect circular dependency chains between files')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--max-depth <n>', 'Maximum cycle depth', parseIntSafe, 10)\n  .action((opts) => {\n    runQuery(\n      (db) => queries.cycles(db, { scope: opts.scope, maxDepth: opts.maxDepth }),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No circular dependencies found.');\n        } else {\n          for (let i = 0; i < results.length; i++) {\n            console.log(`\\nCycle ${i + 1} (${results[i]!.path.length - 1} files):`);\n            for (let j = 0; j < results[i]!.path.length; j++) {\n              const arrow = j < results[i]!.path.length - 1 ? ' →' : ' (cycle)';\n              console.log(`  ${results[i]!.path[j]}${arrow}`);\n            }\n          }\n          console.log(`\\n${results.length} cycle(s) found.`);\n        }\n      },\n    );\n  });\n\n// bottlenecks\nprogram\n  .command('bottlenecks')\n  .description('Find coupling hubs: high fan-in AND high fan-out')\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 20)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-fan-in <n>', 'Minimum fan-in', parseIntSafe, 2)\n  .option('--min-fan-out <n>', 'Minimum fan-out', parseIntSafe, 2)\n  .action((opts) => {\n    runQuery(\n      (db) => queries.bottlenecks(db, {\n        limit: opts.limit,\n        scope: opts.scope,\n        minFanIn: opts.minFanIn,\n        minFanOut: opts.minFanOut,\n      }),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No bottlenecks found.');\n        } else {\n          console.log('  score  fan-in  fan-out  symbol');\n          console.log('  ─────  ──────  ───────  ──────');\n          for (const r of results) {\n            console.log(`  ${String(r.score).padStart(5)}  ${String(r.fanIn).padStart(6)}  ${String(r.fanOut).padStart(7)}  ${r.shortName}`);\n          }\n        }\n      },\n    );\n  });\n\n// isolated\nprogram\n  .command('isolated')\n  .description('Find completely orphaned symbols (no references at all)')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-loc <n>', 'Minimum lines of code', parseIntSafe, 3)\n  .action((opts) => {\n    runQuery(\n      (db) => queries.isolated(db, { scope: opts.scope, minLoc: opts.minLoc }),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No isolated symbols found.');\n        } else {\n          let prevFile = '';\n          for (const r of results) {\n            if (r.relativePath !== prevFile) {\n              if (prevFile) console.log('');\n              console.log(r.relativePath);\n              prevFile = r.relativePath;\n            }\n            console.log(`  ${r.startLine}-${r.endLine}  (${r.loc} LOC)  ${r.shortName}`);\n          }\n          console.log(`\\n${results.length} isolated symbol(s)`);\n        }\n      },\n    );\n  });\n\n// by-kind\nprogram\n  .command('by-kind <kind>')\n  .description('Find symbols by SCIP kind (class, interface, enum, function, etc.)')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 100)\n  .action((kind, opts) => {\n    runQuery(\n      (db) => queries.byKind(db, kind, { scope: opts.scope, limit: opts.limit }),\n      (results) => {\n        if (results.length === 0) {\n          console.log(`No symbols found for kind \"${kind}\". Use \"kind-counts\" to see available kinds.`);\n        } else {\n          for (const r of results) {\n            console.log(`  ${r.relativePath}:${r.startLine}-${r.endLine}  [${r.kindName}]  ${r.shortName}`);\n          }\n          console.log(`\\n${results.length} symbol(s)`);\n        }\n      },\n    );\n  });\n\n// kind-counts\nprogram\n  .command('kind-counts')\n  .description('Histogram of symbol kinds in the codebase')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .action((opts) => {\n    runQuery(\n      (db) => queries.kindCounts(db, { scope: opts.scope }),\n      (results) => {\n        console.log('  count  kind');\n        console.log('  ─────  ────');\n        for (const r of results) {\n          console.log(`  ${String(r.count).padStart(5)}  ${r.kindName} (${r.kind})`);\n        }\n      },\n    );\n  });\n\n// test-coverage\nprogram\n  .command('test-coverage [symbol]')\n  .description('Check if symbols are referenced by test files')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-loc <n>', 'Minimum LOC for summary mode', parseIntSafe, 3)\n  .action((symbol, opts) => {\n    withDb((db) => {\n      if (symbol) {\n        const results = queries.testCoverage(db, symbol);\n        for (const r of results) {\n          const status = r.covered ? 'covered' : 'NOT COVERED';\n          console.log(`  [${status}]  ${r.shortName}  (${r.definedIn})`);\n          for (const tf of r.testFiles) {\n            console.log(`    ← ${tf}`);\n          }\n        }\n      } else {\n        const summary = queries.testCoverageSummary(db, { scope: opts.scope, minLoc: opts.minLoc });\n        console.log(`Test coverage: ${summary.percent}%`);\n        console.log(`  Total symbols:  ${summary.total}`);\n        console.log(`  Covered:        ${summary.covered}`);\n        console.log(`  Not covered:    ${summary.uncovered}`);\n      }\n    });\n  });\n\n// doc-coverage\nprogram\n  .command('doc-coverage')\n  .description('Check documentation coverage across symbols')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-loc <n>', 'Minimum LOC to consider', parseIntSafe, 3)\n  .option('-n, --limit <n>', 'Max undocumented symbols to show', parseIntSafe, 50)\n  .action((opts) => {\n    runQuery(\n      (db) => queries.docCoverage(db, {\n        scope: opts.scope,\n        minLoc: opts.minLoc,\n        limit: opts.limit,\n      }),\n      (result) => {\n        console.log(`Documentation coverage: ${result.coveragePercent}%`);\n        console.log(`  Total symbols:   ${result.totalSymbols}`);\n        console.log(`  Documented:      ${result.documented}`);\n        console.log(`  Undocumented:    ${result.undocumented}`);\n        if (result.undocumentedSymbols.length > 0) {\n          console.log('\\nUndocumented:');\n          for (const s of result.undocumentedSymbols) {\n            console.log(`  ${s.relativePath}:${s.startLine}  ${s.shortName}`);\n          }\n        }\n      },\n    );\n  });\n\n// deep-chains\nprogram\n  .command('deep-chains')\n  .description('Find the longest transitive dependency chains')\n  .option('-n, --limit <n>', 'Number of chains to show', parseIntSafe, 10)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-depth <n>', 'Minimum chain depth', parseIntSafe, 3)\n  .action((opts) => {\n    runQuery(\n      (db) => queries.deepChains(db, {\n        limit: opts.limit,\n        scope: opts.scope,\n        minDepth: opts.minDepth,\n      }),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No deep chains found.');\n        } else {\n          for (let i = 0; i < results.length; i++) {\n            console.log(`\\nChain ${i + 1} (depth ${results[i]!.depth}):`);\n            for (const file of results[i]!.chain) {\n              console.log(`  → ${file}`);\n            }\n          }\n        }\n      },\n    );\n  });\n\n// hierarchy\nprogram\n  .command('hierarchy <symbol>')\n  .description('Show a symbol\\'s ancestry chain (method → class → module)')\n  .action((symbol) => {\n    runQuery(\n      (db) => queries.hierarchy(db, symbol),\n      (chain) => {\n        if (chain.length === 0) {\n          console.log('Symbol not found.');\n        } else {\n          for (const node of chain) {\n            const indent = '  '.repeat(node.depth);\n            console.log(`${indent}${node.shortName}`);\n          }\n        }\n      },\n    );\n  });\n\n// call-graph\nprogram\n  .command('call-graph <symbol>')\n  .description('Show incoming callers and outgoing callees for a symbol')\n  .action((symbol) => {\n    runQuery(\n      (db) => queries.callGraph(db, symbol),\n      (result) => {\n        if (!result) {\n          console.log('Symbol not found.');\n          return;\n        }\n        console.log(`Symbol: ${result.shortName}\\n`);\n        console.log(`═══ CALLERS (${result.callers.length}) ═══`);\n        for (const c of result.callers) {\n          console.log(`  ${c.file}  ${c.shortName}`);\n        }\n        console.log(`\\n═══ CALLEES (${result.callees.length}) ═══`);\n        for (const c of result.callees) {\n          console.log(`  ${c.file}  ${c.shortName}`);\n        }\n      },\n    );\n  });\n\n// similar\nprogram\n  .command('similar [symbol]')\n  .description('Find functions with similar callee fingerprints (consolidation candidates)')\n  .option('--min-similarity <n>', 'Minimum Jaccard similarity (0-1)', parseFloat, 0.4)\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 20)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-callees <n>', 'Minimum callees to consider', parseIntSafe, 4)\n  .action((symbol, opts) => {\n    withDb((db) => {\n      if (symbol) {\n        const results = queries.similar(db, symbol, {\n          minSimilarity: opts.minSimilarity,\n          limit: opts.limit,\n        });\n        if (results.length === 0) {\n          console.log('No similar symbols found.');\n        } else {\n          for (const r of results) {\n            console.log(`\\n${Math.round(r.similarity * 100)}% similar:`);\n            console.log(`  A: ${r.shortNameA}  (${r.fileA})`);\n            console.log(`  B: ${r.shortNameB}  (${r.fileB})`);\n            console.log(`  Shared callees: ${r.sharedCallees.join(', ')}`);\n            if (r.uniqueToA.length) console.log(`  Only in A: ${r.uniqueToA.join(', ')}`);\n            if (r.uniqueToB.length) console.log(`  Only in B: ${r.uniqueToB.join(', ')}`);\n          }\n        }\n      } else {\n        const results = queries.similarAll(db, {\n          minSimilarity: opts.minSimilarity,\n          limit: opts.limit,\n          scope: opts.scope,\n          minCallees: opts.minCallees,\n        });\n        if (results.length === 0) {\n          console.log('No similar symbol pairs found.');\n        } else {\n          for (const r of results) {\n            console.log(`\\n${Math.round(r.similarity * 100)}% similar:`);\n            console.log(`  A: ${r.shortNameA}  (${r.fileA})`);\n            console.log(`  B: ${r.shortNameB}  (${r.fileB})`);\n            console.log(`  Shared: ${r.sharedCallees.join(', ')}`);\n          }\n          console.log(`\\n${results.length} similar pair(s) found.`);\n        }\n      }\n    });\n  });\n\n// similar-files\nprogram\n  .command('similar-files [file]')\n  .description('Find files with similar dependency profiles')\n  .option('--min-similarity <n>', 'Minimum Jaccard similarity (0-1)', parseFloat, 0.5)\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 20)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-deps <n>', 'Minimum dependencies to consider', parseIntSafe, 3)\n  .action((file, opts) => {\n    runQuery(\n      (db) => queries.similarFiles(db, {\n        minSimilarity: opts.minSimilarity,\n        limit: opts.limit,\n        scope: opts.scope,\n        minDeps: opts.minDeps,\n        filePattern: file,\n      }),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No similar file pairs found.');\n        } else {\n          for (const r of results) {\n            console.log(`\\n${Math.round(r.similarity * 100)}% similar:`);\n            console.log(`  ${r.fileA}`);\n            console.log(`  ${r.fileB}`);\n            console.log(`  Shared deps (${r.sharedDeps.length}): ${r.sharedDeps.join(', ')}`);\n            if (r.uniqueToA.length) console.log(`  Only in first:  ${r.uniqueToA.join(', ')}`);\n            if (r.uniqueToB.length) console.log(`  Only in second: ${r.uniqueToB.join(', ')}`);\n          }\n          console.log(`\\n${results.length} similar pair(s) found.`);\n        }\n      },\n    );\n  });\n\n// similar-chains\nprogram\n  .command('similar-chains')\n  .description('Find end-to-end dependency flows that diverge at few points')\n  .option('--min-similarity <n>', 'Minimum chain similarity (0-1)', parseFloat, 0.5)\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 15)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-length <n>', 'Minimum chain length', parseIntSafe, 3)\n  .option('--max-length <n>', 'Maximum chain length', parseIntSafe, 8)\n  .action((opts) => {\n    runQuery(\n      (db) => queries.similarChains(db, {\n        minSimilarity: opts.minSimilarity,\n        limit: opts.limit,\n        scope: opts.scope,\n        minChainLength: opts.minLength,\n        maxChainLength: opts.maxLength,\n      }),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No similar chains found.');\n        } else {\n          for (let i = 0; i < results.length; i++) {\n            const r = results[i]!;\n            console.log(`\\n── Chain pair ${i + 1} (${Math.round(r.similarity * 100)}% similar, ${r.divergencePoints.length} divergence point(s)) ──`);\n            console.log(`  Chain A: ${r.chainA.join(' → ')}`);\n            console.log(`  Chain B: ${r.chainB.join(' → ')}`);\n            if (r.commonPrefix.length) console.log(`  Common prefix: ${r.commonPrefix.join(' → ')}`);\n            if (r.commonSuffix.length) console.log(`  Common suffix: ${r.commonSuffix.join(' → ')}`);\n            console.log('  Divergence points (consolidation targets):');\n            for (const d of r.divergencePoints) {\n              console.log(`    [${d.index}] ${d.nodeA}  ↔  ${d.nodeB}`);\n            }\n          }\n          console.log(`\\n${results.length} similar chain pair(s) found.`);\n        }\n      },\n    );\n  });\n\n// extract-candidates\nprogram\n  .command('extract-candidates')\n  .description('Find functions with natural extraction seams (isolated callee clusters)')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-loc <n>', 'Minimum function LOC', parseIntSafe, 10)\n  .option('--min-callees <n>', 'Minimum callees to analyze', parseIntSafe, 6)\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 20)\n  .action((opts) => {\n    runQuery(\n      (db) => queries.extractCandidates(db, {\n        scope: opts.scope,\n        minLoc: opts.minLoc,\n        minCallees: opts.minCallees,\n        limit: opts.limit,\n      }),\n      (results) => {\n        if (results.length === 0) {\n          console.log('No extraction candidates found.');\n        } else {\n          for (const r of results) {\n            console.log(`\\n${r.relativePath}:${r.startLine}-${r.endLine}  ${r.shortName}  (${r.loc} LOC, ${r.totalCallees} callees)`);\n            for (let i = 0; i < r.clusters.length; i++) {\n              const c = r.clusters[i]!;\n              console.log(`  Cluster ${i + 1} (${Math.round(c.isolation * 100)}% isolated, ${c.callees.length} callees):`);\n              for (const callee of c.callees) {\n                console.log(`    ${callee}`);\n              }\n            }\n          }\n          console.log(`\\n${results.length} extraction candidate(s) found.`);\n        }\n      },\n    );\n  });\n\n// affected\nprogram\n  .command('affected <symbol>')\n  .description('Transitive closure of symbols that could break if this symbol changes')\n  .option('--max-depth <n>', 'Maximum traversal depth', parseIntSafe, 5)\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .action((symbol, opts) => {\n    const db = openDb();\n    const results = queries.affected(db, symbol, { maxDepth: opts.maxDepth, scope: opts.scope });\n    if (results.length === 0) {\n      console.log('No affected symbols found.');\n    } else {\n      let prevDepth = -1;\n      for (const r of results) {\n        if (r.depth !== prevDepth) {\n          console.log(`\\n  ── Depth ${r.depth} ──`);\n          prevDepth = r.depth;\n        }\n        console.log(`  ${r.file}  ${r.shortName}`);\n      }\n      console.log(`\\n${results.length} affected symbol(s) across ${new Set(results.map((r) => r.file)).size} files.`);\n    }\n    db.close();\n  });\n\n// change-surface\nprogram\n  .command('change-surface <file>')\n  .description('Pre-change briefing: exports, consumers, test coverage, risk')\n  .action((file) => {\n    const db = openDb();\n    const result = queries.changeSurface(db, file);\n    if (!result) {\n      console.log('File not found in index.');\n      db.close();\n      return;\n    }\n    console.log(`File: ${result.file}`);\n    console.log(`Test coverage: ${result.testCoveragePercent}% | External consumers: ${result.totalExternalConsumers}\\n`);\n    for (const s of result.symbols) {\n      const risk = s.riskLevel === 'high' ? ' *** HIGH RISK ***' : s.riskLevel === 'medium' ? ' * medium risk *' : '';\n      const tests = s.testFiles.length > 0 ? ` (${s.testFiles.length} test file(s))` : ' (no tests)';\n      console.log(`  ${s.startLine}-${s.endLine}  ${s.shortName}  [${s.externalConsumers} consumers]${tests}${risk}`);\n    }\n    db.close();\n  });\n\n// diff-impact\nprogram\n  .command('diff-impact')\n  .description('Compute affected symbols from current git diff')\n  .option('--base <ref>', 'Git ref to diff against (default: HEAD)')\n  .action((opts) => {\n    const db = openDb();\n    const result = queries.diffImpact(db, { base: opts.base });\n    console.log(`Changed files: ${result.summary.totalChangedFiles}`);\n    console.log(`Changed symbols: ${result.summary.totalChangedSymbols}`);\n    console.log(`Affected consumer files: ${result.summary.totalAffectedFiles}`);\n    console.log(`Test coverage: ${result.summary.testCoveragePercent}%\\n`);\n    if (result.changedSymbols.length > 0) {\n      console.log('Changed symbols:');\n      for (const s of result.changedSymbols) {\n        console.log(`  ${s.file}  ${s.shortName}  (fan-in: ${s.fanIn})`);\n      }\n    }\n    if (result.uncoveredSymbols.length > 0) {\n      console.log('\\nUncovered (no test references):');\n      for (const s of result.uncoveredSymbols) {\n        console.log(`  ${s.file}  ${s.shortName}`);\n      }\n    }\n    if (result.affectedConsumers.length > 0) {\n      console.log('\\nAffected consumer files:');\n      for (const c of result.affectedConsumers) {\n        console.log(`  ${c.file}  (${c.consumedSymbols} symbol(s))`);\n      }\n    }\n    db.close();\n  });\n\n// drift\nprogram\n  .command('drift [module]')\n  .description('Detect unused imports, layer violations, and pattern deviations')\n  .action((module) => {\n    const db = openDb();\n    const summary = queries.drift(db, { scope: module });\n    if (summary.results.length === 0) {\n      console.log('No drift detected.');\n    } else {\n      const grouped = new Map<string, typeof summary.results>();\n      for (const r of summary.results) {\n        if (!grouped.has(r.file)) grouped.set(r.file, []);\n        grouped.get(r.file)!.push(r);\n      }\n      for (const [file, items] of grouped) {\n        console.log(`\\n${file}`);\n        for (const r of items) {\n          const tag = r.kind === 'unused-import' ? 'UNUSED' : r.kind === 'layer-violation' ? 'LAYER' : 'UNIQUE';\n          console.log(`  [${tag}] ${r.description}`);\n          if (r.detail) console.log(`         ${r.detail}`);\n        }\n      }\n      console.log(`\\n${summary.unusedImports} unused import(s), ${summary.layerViolations} layer violation(s), ${summary.patternDeviations} pattern deviation(s)`);\n    }\n    db.close();\n  });\n\n// wrapper-candidates\nprogram\n  .command('wrapper-candidates')\n  .description('Find symbols only called by one consumer (premature abstractions)')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--max-loc <n>', 'Maximum LOC for candidates', parseIntSafe, 15)\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 30)\n  .action((opts) => {\n    const db = openDb();\n    const results = queries.wrapperCandidates(db, { scope: opts.scope, maxLoc: opts.maxLoc, limit: opts.limit });\n    if (results.length === 0) {\n      console.log('No wrapper candidates found.');\n    } else {\n      for (const r of results) {\n        console.log(`  ${r.file}:${r.startLine}-${r.endLine}  ${r.shortName}  (${r.loc} LOC)`);\n        console.log(`    Only called by: ${r.singleCallerShort}  (fan-in: ${r.callerFanIn})`);\n      }\n      console.log(`\\n${results.length} wrapper candidate(s).`);\n    }\n    db.close();\n  });\n\n// passthrough-candidates\nprogram\n  .command('passthrough-candidates')\n  .description('Find functions that just forward to one other function')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--max-loc <n>', 'Maximum LOC for candidates', parseIntSafe, 15)\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 30)\n  .action((opts) => {\n    const db = openDb();\n    const results = queries.passthroughCandidates(db, { scope: opts.scope, maxLoc: opts.maxLoc, limit: opts.limit });\n    if (results.length === 0) {\n      console.log('No passthrough candidates found.');\n    } else {\n      for (const r of results) {\n        console.log(`  ${r.file}:${r.startLine}-${r.endLine}  ${r.shortName}  (${r.loc} LOC)`);\n        console.log(`    Forwards to: ${r.forwardsToShort}  (${r.forwardsToFile})`);\n      }\n      console.log(`\\n${results.length} passthrough candidate(s).`);\n    }\n    db.close();\n  });\n\n// stale-abstractions\nprogram\n  .command('stale-abstractions')\n  .description('Find types/interfaces with 0-1 consumers (premature abstractions)')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-loc <n>', 'Minimum LOC', parseIntSafe, 3)\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 30)\n  .action((opts) => {\n    const db = openDb();\n    const results = queries.staleAbstractions(db, { scope: opts.scope, minLoc: opts.minLoc, limit: opts.limit });\n    if (results.length === 0) {\n      console.log('No stale abstractions found.');\n    } else {\n      for (const r of results) {\n        const label = r.consumers === 0 ? 'unused' : '1 consumer';\n        console.log(`  ${r.file}:${r.startLine}-${r.endLine}  ${r.shortName}  (${r.loc} LOC, ${label})`);\n      }\n      console.log(`\\n${results.length} stale abstraction(s).`);\n    }\n    db.close();\n  });\n\n// complexity-hotspots\nprogram\n  .command('complexity-hotspots')\n  .description('Composite complexity score: LOC x fan-in x fan-out')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-loc <n>', 'Minimum LOC', parseIntSafe, 10)\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 20)\n  .action((opts) => {\n    const db = openDb();\n    const results = queries.complexityHotspots(db, { scope: opts.scope, minLoc: opts.minLoc, limit: opts.limit });\n    if (results.length === 0) {\n      console.log('No complexity hotspots found.');\n    } else {\n      console.log('  score   LOC  fan-in  fan-out  callees  symbol');\n      console.log('  ─────  ────  ──────  ───────  ───────  ──────');\n      for (const r of results) {\n        console.log(`  ${r.score.toFixed(1).padStart(5)}  ${String(r.loc).padStart(4)}  ${String(r.fanIn).padStart(6)}  ${String(r.fanOut).padStart(7)}  ${String(r.calleeCount).padStart(7)}  ${r.shortName}`);\n      }\n    }\n    db.close();\n  });\n\n// health\nprogram\n  .command('health')\n  .description('Composite codebase health report with prioritized action list')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--json', 'Output as JSON for programmatic consumption')\n  .action((opts) => {\n    const db = openDb();\n    const report = queries.health(db, { scope: opts.scope });\n    if (opts.json) {\n      console.log(JSON.stringify(report, null, 2));\n    } else {\n      console.log(`\\n  Codebase Health Score: ${report.score}/100\\n`);\n      console.log(`  ${report.overview.documents} files | ${report.overview.symbols} symbols | ${formatBytes(report.overview.indexSizeBytes)}\\n`);\n\n      console.log('  Findings:');\n      const f = report.findings;\n      if (f.deadSymbols > 0) console.log(`    Dead code:            ${f.deadSymbols} symbols (${f.deadLoc} LOC)`);\n      if (f.isolatedSymbols > 0) console.log(`    Isolated symbols:     ${f.isolatedSymbols} (${f.isolatedLoc} LOC)`);\n      if (f.cycles > 0) console.log(`    Circular deps:        ${f.cycles}`);\n      if (f.similarPairs > 0) console.log(`    Similar pairs:        ${f.similarPairs}`);\n      if (f.extractionCandidates > 0) console.log(`    Extract candidates:   ${f.extractionCandidates}`);\n      if (f.wrappers > 0) console.log(`    Wrapper functions:    ${f.wrappers}`);\n      if (f.passthroughs > 0) console.log(`    Passthroughs:         ${f.passthroughs}`);\n      if (f.staleTypes > 0) console.log(`    Stale abstractions:   ${f.staleTypes}`);\n      if (f.driftedFiles > 0) console.log(`    Pattern drift:        ${f.driftedFiles} files`);\n      if (f.complexityHotspotCount > 0) console.log(`    Complexity hotspots:  ${f.complexityHotspotCount}`);\n      console.log(`    Test coverage:        ${f.testCoveragePercent}%`);\n\n      if (report.actions.length > 0) {\n        console.log('\\n  Prioritized Actions (highest impact + lowest effort first):');\n        for (let i = 0; i < report.actions.length; i++) {\n          const a = report.actions[i]!;\n          const loc = a.locRecoverable > 0 ? ` (~${a.locRecoverable} LOC recoverable)` : '';\n          console.log(`    ${i + 1}. [${a.effort} effort / ${a.impact} impact] ${a.description}${loc}`);\n        }\n      }\n\n      if (report.topComplexity.length > 0) {\n        console.log('\\n  Top Complexity Hotspots:');\n        for (const c of report.topComplexity) {\n          console.log(`    ${c.score.toFixed(1).padStart(6)}  ${c.symbol}`);\n        }\n      }\n\n      if (report.actions.length === 0) {\n        console.log('\\n  No issues found. Codebase is clean.');\n      }\n    }\n    db.close();\n  });\n\n// convergence\nprogram\n  .command('convergence <symbol1> <symbol2>')\n  .description('Show what a consolidated version of two similar functions would look like')\n  .action((symbol1, symbol2) => {\n    const db = openDb();\n    const result = queries.convergence(db, symbol1, symbol2);\n    if (!result) {\n      console.log('One or both symbols not found.');\n      db.close();\n      return;\n    }\n    console.log(`\\n${Math.round(result.similarity * 100)}% callee overlap\\n`);\n    console.log(`  A: ${result.symbolA.shortName}  (${result.symbolA.file}, ${result.symbolA.loc} LOC)`);\n    console.log(`  B: ${result.symbolB.shortName}  (${result.symbolB.file}, ${result.symbolB.loc} LOC)\\n`);\n    console.log(`  Shared callees (${result.sharedCallees.length}):`);\n    for (const c of result.sharedCallees) console.log(`    ${c}`);\n    if (result.uniqueToA.length > 0) {\n      console.log(`\\n  Unique to A (${result.uniqueToA.length}):`);\n      for (const c of result.uniqueToA) console.log(`    ${c}`);\n    }\n    if (result.uniqueToB.length > 0) {\n      console.log(`\\n  Unique to B (${result.uniqueToB.length}):`);\n      for (const c of result.uniqueToB) console.log(`    ${c}`);\n    }\n    console.log(`\\n  Strategy: ${result.consolidationStrategy}`);\n    db.close();\n  });\n\n// code\nprogram\n  .command('code <symbol>')\n  .description('Read the source code for a symbol (bounded to its definition range)')\n  .option('-C, --context <n>', 'Extra lines of context above/below', parseIntSafe, 0)\n  .action((symbol, opts) => {\n    const db = openDb();\n    const result = queries.code(db, symbol, { context: opts.context });\n    if (!result) {\n      console.log('Symbol not found or file unreadable.');\n      db.close();\n      return;\n    }\n    console.log(`${result.relativePath}:${result.startLine}-${result.endLine}  ${result.shortName}  [${result.language ?? 'unknown'}]\\n`);\n    const lines = result.source.split('\\n');\n    for (let i = 0; i < lines.length; i++) {\n      console.log(`  ${String(result.startLine + i).padStart(4)}  ${lines[i]}`);\n    }\n    db.close();\n  });\n\n// complexity\nprogram\n  .command('complexity <symbol>')\n  .description('Per-symbol complexity: branches, cyclomatic estimate, fan-in/out, callees')\n  .action((symbol) => {\n    const db = openDb();\n    const result = queries.complexity(db, symbol);\n    if (!result) {\n      console.log('Symbol not found.');\n      db.close();\n      return;\n    }\n    console.log(`${result.relativePath}:${result.startLine}-${result.endLine}  ${result.shortName}\\n`);\n    console.log(`  LOC:                  ${result.loc}`);\n    console.log(`  Branches:             ${result.branches}`);\n    console.log(`  Cyclomatic estimate:  ${result.cyclomaticEstimate}`);\n    console.log(`  Callees:              ${result.calleeCount}`);\n    console.log(`  Fan-in:               ${result.fanIn}`);\n    console.log(`  Fan-out:              ${result.fanOut}`);\n    db.close();\n  });\n\n// dataflow\nprogram\n  .command('dataflow <symbol>')\n  .description('Reference-level dataflow: definition sites, usage sites, producers, consumers')\n  .action((symbol) => {\n    const db = openDb();\n    const result = queries.dataflow(db, symbol);\n    if (!result) {\n      console.log('Symbol not found.');\n      db.close();\n      return;\n    }\n    console.log(`${result.shortName}  (${result.relativePath})\\n`);\n\n    if (result.definitionSites.length > 0) {\n      console.log('  ═══ DEFINED AT ═══');\n      for (const s of result.definitionSites) {\n        console.log(`    ${s.file}:${s.line}`);\n      }\n    }\n\n    if (result.usageSites.length > 0) {\n      console.log('\\n  ═══ USED AT ═══');\n      for (const s of result.usageSites) {\n        console.log(`    ${s.file}:${s.line}  in ${s.enclosingShort}`);\n      }\n    }\n\n    if (result.producers.length > 0) {\n      console.log('\\n  ═══ PRODUCERS (feeds into this) ═══');\n      for (const p of result.producers) {\n        console.log(`    ${p.file}  ${p.shortName}`);\n      }\n    }\n\n    if (result.consumers.length > 0) {\n      console.log('\\n  ═══ CONSUMERS (this feeds into) ═══');\n      for (const c of result.consumers) {\n        console.log(`    ${c.file}  ${c.shortName}`);\n      }\n    }\n    db.close();\n  });\n\n// slice\nprogram\n  .command('slice <symbol>')\n  .description('Reference-level program slice: what affects this (backward) or what this affects (forward)')\n  .option('--forward', 'Forward slice (what does this affect). Default is backward.')\n  .action((symbol, opts) => {\n    const db = openDb();\n    const direction = opts.forward ? 'forward' : 'backward';\n    const result = queries.slice(db, symbol, { direction });\n    if (!result) {\n      console.log('Symbol not found.');\n      db.close();\n      return;\n    }\n    console.log(`${result.direction} slice of ${result.shortName}\\n`);\n    if (result.connectedSymbols.length === 0) {\n      console.log('  No connected symbols found.');\n    } else {\n      for (const s of result.connectedSymbols) {\n        console.log(`  ${s.file}  ${s.shortName}`);\n        console.log(`    ${s.relationship}`);\n      }\n      console.log(`\\n${result.connectedSymbols.length} connected symbol(s).`);\n    }\n    db.close();\n  });\n\n// install-skills\nprogram\n  .command('install-skills')\n  .description('Install skills (concrete-plan, scip-explore, scip-debloat, scip-verify) into Claude Code and Codex')\n  .action(() => {\n    const result = installSkills();\n    const total = result.installed.length + result.alreadyLinked.length;\n    console.log(`\\n${result.installed.length} installed, ${result.alreadyLinked.length} already linked, ${result.skipped.length} skipped.`);\n    if (total > 0) {\n      console.log('Skills will be available in your next Claude Code / Codex session.');\n    }\n  });\n\n// check-deps\nprogram\n  .command('check-deps')\n  .description('Check if required dependencies (scip CLI) are installed')\n  .action(() => {\n    if (isScipInstalled()) {\n      console.log('scip CLI: installed');\n    } else {\n      printScipInstallInstructions();\n    }\n  });\n\n// redundant-reexports\nprogram\n  .command('redundant-reexports')\n  .description('Find barrel re-exports that nobody imports through')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('-n, --limit <n>', 'Number of results', parseIntSafe, 30)\n  .action((opts) => {\n    const db = openDb();\n    const results = queries.redundantReexports(db, { scope: opts.scope, limit: opts.limit });\n    if (results.length === 0) {\n      console.log('No redundant re-exports found.');\n    } else {\n      let prevBarrel = '';\n      for (const r of results) {\n        if (r.barrelFile !== prevBarrel) {\n          if (prevBarrel) console.log('');\n          console.log(r.barrelFile);\n          prevBarrel = r.barrelFile;\n        }\n        console.log(`  ${r.shortName}  (from ${r.originalFile})`);\n        console.log(`    barrel: ${r.barrelConsumers} consumer(s) | direct: ${r.directConsumers} consumer(s)`);\n      }\n      console.log(`\\n${results.length} redundant re-export(s).`);\n    }\n    db.close();\n  });\n\n// similar-signatures\nprogram\n  .command('similar-signatures')\n  .description('Find functions with near-identical type signatures (same shape)')\n  .option('-s, --scope <path>', 'Limit to files matching path')\n  .option('--min-loc <n>', 'Minimum LOC per function', parseIntSafe, 3)\n  .option('-n, --limit <n>', 'Number of groups', parseIntSafe, 20)\n  .action((opts) => {\n    const db = openDb();\n    const groups = queries.similarSignatures(db, { scope: opts.scope, minLoc: opts.minLoc, limit: opts.limit });\n    if (groups.length === 0) {\n      console.log('No same-shape function groups found.');\n    } else {\n      for (const g of groups) {\n        console.log(`\\nSignature: ${g.signature}  (${g.functions.length} functions)`);\n        for (const f of g.functions) {\n          console.log(`  ${f.file}:${f.startLine}-${f.endLine}  ${f.shortName}  (${f.loc} LOC)`);\n        }\n      }\n      console.log(`\\n${groups.length} group(s) found.`);\n    }\n    db.close();\n  });\n\n// init\nprogram\n  .command('init')\n  .description('Create a .scipquery.json config file for this project')\n  .action(() => {\n    const projectRoot = resolveProjectRoot();\n    const languages = detectLanguages(projectRoot);\n    const configPath = initProjectConfig(projectRoot, languages);\n    console.log(`Config written to ${configPath}`);\n    console.log(`Detected languages: ${languages.join(', ') || '(none)'}`);\n  });\n\n// watch\nprogram\n  .command('watch')\n  .description('Watch for file changes and reindex automatically')\n  .option('--debounce <ms>', 'Ms to wait after last change (default: 30000)', parseInt)\n  .option('--cooldown <ms>', 'Min ms between reindexes (default: 60000)', parseInt)\n  .action((opts) => {\n    const projectRoot = resolveProjectRoot();\n    const config = loadProjectConfig(projectRoot);\n\n    // CLI flags override config\n    if (opts.debounce) (config.watch ??= {}).debounceMs = opts.debounce;\n    if (opts.cooldown) (config.watch ??= {}).cooldownMs = opts.cooldown;\n\n    const watcher = new Watcher({\n      projectRoot,\n      config,\n      onStatus: (status) => {\n        process.stdout.write(`\\r\\x1b[K${formatStatus(status)}`);\n      },\n      onReindexComplete: (durationMs) => {\n        console.log(`\\nReindex complete in ${(durationMs / 1000).toFixed(1)}s`);\n      },\n      onError: (err) => {\n        console.error(`\\nWatch error: ${err.message}`);\n      },\n    });\n\n    console.log(`Watching ${projectRoot}`);\n    console.log(`Debounce: ${config.watch?.debounceMs ?? 30000}ms | Cooldown: ${config.watch?.cooldownMs ?? 60000}ms`);\n    console.log('Press Ctrl+C to stop.\\n');\n    watcher.start();\n\n    process.on('SIGINT', () => {\n      watcher.stop();\n      console.log('\\nStopped.');\n      process.exit(0);\n    });\n  });\n\n// status\nprogram\n  .command('status')\n  .description('Show index status for this project')\n  .action(() => {\n    const projectRoot = resolveProjectRoot();\n    const config = loadProjectConfig(projectRoot);\n    const paths = resolveIndexPaths(projectRoot, config);\n\n    console.log(`Project:  ${projectRoot}`);\n    console.log(`DB path:  ${paths.dbPath}`);\n    console.log(`Exists:   ${existsSync(paths.dbPath) ? 'yes' : 'no'}`);\n\n    if (existsSync(paths.dbPath)) {\n      withDb((db) => {\n        const s = queries.stats(db);\n        console.log(`Symbols:  ${s.symbols}`);\n        console.log(`Files:    ${s.documents}`);\n        console.log(`Size:     ${formatBytes(s.indexSizeBytes)}`);\n        if (s.lastBuilt) {\n          const ago = Math.round((Date.now() - s.lastBuilt.getTime()) / 1000);\n          console.log(`Built:    ${ago}s ago`);\n        }\n      });\n    }\n  });\n\n// ── Parse & Run ────────────────────────────────────────────\n\nprogram.parse();\n\n// ── Utility ────────────────────────────────────────────────\n\nfunction collect(value: string, prev: string[]): string[] {\n  return prev.concat([value]);\n}\n\n/** parseInt wrapper safe for commander (which passes default as 2nd arg = radix) */\nfunction parseIntSafe(value: string): number {\n  return parseInt(value, 10);\n}\n\nfunction formatBytes(bytes: number): string {\n  if (bytes < 1024) return `${bytes} B`;\n  if (bytes < 1024 * 1024) return `${(bytes / 1024).toFixed(0)} KB`;\n  if (bytes < 1024 * 1024 * 1024) return `${(bytes / (1024 * 1024)).toFixed(1)} MB`;\n  return `${(bytes / (1024 * 1024 * 1024)).toFixed(1)} GB`;\n}\n\nfunction formatStatus(status: WatcherStatus): string {\n  switch (status.state) {\n    case 'idle':\n      return 'Watching (idle)';\n    case 'waiting': {\n      const secs = Math.round((status.reindexAt - Date.now()) / 1000);\n      return `${status.changedFiles} file(s) changed, reindexing in ${secs}s...`;\n    }\n    case 'indexing':\n      return `Reindexing... (${Math.round((Date.now() - status.startedAt) / 1000)}s)`;\n    case 'cooldown': {\n      const secs = Math.round((status.until - Date.now()) / 1000);\n      return `Cooldown (${secs}s)${status.dirty ? ' — changes pending' : ''}`;\n    }\n  }\n}\n","import Database from 'better-sqlite3';\nimport { statSync } from 'node:fs';\nimport type { PathFilter } from './gitignore-filter.js';\nimport type { ScipQueryConfig } from './types.js';\n\n/**\n * Thin wrapper around better-sqlite3 with a pre-configured connection\n * and helper methods for the SCIP SQLite schema.\n *\n * The schema is produced by `scip expt-convert` and is identical\n * regardless of source language (TypeScript, Rust, Python, etc.).\n *\n * Tables:\n *   documents             — indexed files (id, language, relative_path)\n *   global_symbols        — all symbols (id, symbol, display_name, kind, documentation)\n *   defn_enclosing_ranges — definition locations (document_id, symbol_id, start/end line/char)\n *   mentions              — references & definitions (chunk_id, symbol_id, role)\n *   chunks                — code segments (document_id, chunk_index, start/end line, occurrences)\n */\nexport class ScipDatabase {\n  readonly db: Database.Database;\n  readonly config: ScipQueryConfig;\n  private pathFilter: PathFilter | null;\n\n  constructor(config: ScipQueryConfig, pathFilter?: PathFilter) {\n    this.config = config;\n    this.pathFilter = pathFilter ?? null;\n    this.db = new Database(config.dbPath, { readonly: true });\n    this.db.pragma('busy_timeout = 5000');\n  }\n\n  /** Attach a gitignore-based path filter for query results */\n  setPathFilter(filter: PathFilter): void {\n    this.pathFilter = filter;\n  }\n\n  /** Check if a path should be excluded based on .gitignore rules */\n  isIgnored(relativePath: string): boolean {\n    return this.pathFilter?.isIgnored(relativePath) ?? false;\n  }\n\n  /** Filter an array of paths using the gitignore filter */\n  filterPaths(paths: string[]): string[] {\n    return this.pathFilter?.filter(paths) ?? paths;\n  }\n\n  /**\n   * The local-symbol predicate: only match symbols that are defined\n   * in files NOT excluded by gitignore. This replaces the old hardcoded\n   * `NOT LIKE 'node_modules/%'` check.\n   *\n   * Since SQLite can't evaluate JS gitignore rules inline, we use a\n   * simpler approach: query broadly, then filter in JS. For queries\n   * that need SQL-level filtering, use excludedPathPatterns().\n   */\n  get localSymbolPredicate(): string {\n    // Basic SQL-level exclusions for the most common cases.\n    // JS-level gitignore filtering handles the rest post-query.\n    return `EXISTS (\n      SELECT 1\n      FROM defn_enclosing_ranges local_der\n      JOIN documents local_d ON local_der.document_id = local_d.id\n      WHERE local_der.symbol_id = gs.id\n        ${this.pathExclusionsFor('local_d').trimStart()}\n    )`;\n  }\n\n  /**\n   * SQL WHERE clause fragments to exclude common build/dependency paths.\n   * Complements the JS-level gitignore filtering for performance.\n   */\n  get pathExclusions(): string {\n    return this.pathExclusionsFor('d');\n  }\n\n  /** Reusable SQL fragment: filter out synthetic/internal symbol noise */\n  get symbolNoise(): string {\n    return this.symbolNoiseFor('gs');\n  }\n\n  /** Build SQL path exclusions for one or more document table aliases */\n  pathExclusionsFor(...aliases: string[]): string {\n    return aliases\n      .flatMap((alias) => [\n        `AND ${alias}.relative_path NOT LIKE 'node_modules/%'`,\n        `AND ${alias}.relative_path NOT LIKE '.git/%'`,\n      ])\n      .join('\\n      ');\n  }\n\n  /** Build SQL symbol exclusions for the given global_symbols alias */\n  symbolNoiseFor(alias: string): string {\n    return `AND ${alias}.symbol NOT LIKE '%().(%' AND ${alias}.symbol NOT LIKE '%typeLiteral%'`;\n  }\n\n  /** Run a raw SQL query and return all rows */\n  all<T = Record<string, unknown>>(sql: string, ...params: unknown[]): T[] {\n    return this.db.prepare(sql).all(...params) as T[];\n  }\n\n  /** Run a raw SQL query and return the first row */\n  get<T = Record<string, unknown>>(sql: string, ...params: unknown[]): T | undefined {\n    return this.db.prepare(sql).get(...params) as T | undefined;\n  }\n\n  /** Get the database file size in bytes */\n  sizeBytes(): number {\n    try {\n      return statSync(this.config.dbPath).size;\n    } catch {\n      return 0;\n    }\n  }\n\n  /** Get the last modification time of the database file */\n  lastModified(): Date | null {\n    try {\n      return statSync(this.config.dbPath).mtime;\n    } catch {\n      return null;\n    }\n  }\n\n  close(): void {\n    this.db.close();\n  }\n}\n","import ignore, { type Ignore } from 'ignore';\nimport { readFileSync, existsSync } from 'node:fs';\nimport { join, dirname } from 'node:path';\n\n/**\n * Builds a gitignore-based path filter from .gitignore files found\n * in the project directory tree. This replaces hardcoded path exclusions\n * like \"node_modules/\", \"dist/\", \"target/\", \"__pycache__/\" — instead,\n * we respect whatever the project already ignores.\n *\n * Falls back to sensible defaults if no .gitignore is found.\n */\nexport function createGitignoreFilter(projectRoot: string): PathFilter {\n  const ig = ignore();\n  let loaded = false;\n\n  // Walk up from project root looking for .gitignore files\n  // (nested .gitignore files apply to their subdirectory)\n  const gitignorePaths = findGitignoreFiles(projectRoot);\n\n  for (const gitignorePath of gitignorePaths) {\n    try {\n      const content = readFileSync(gitignorePath, 'utf-8');\n      ig.add(content);\n      loaded = true;\n    } catch {\n      // Skip unreadable files\n    }\n  }\n\n  // If no .gitignore found, use universal defaults\n  if (!loaded) {\n    ig.add(DEFAULT_IGNORES);\n  }\n\n  return {\n    isIgnored: (relativePath: string) => ig.ignores(relativePath),\n    filter: (paths: string[]) => paths.filter((p) => !ig.ignores(p)),\n  };\n}\n\nexport interface PathFilter {\n  /** Returns true if this path should be excluded from results */\n  isIgnored: (relativePath: string) => boolean;\n  /** Filter an array of paths, keeping only non-ignored ones */\n  filter: (paths: string[]) => string[];\n}\n\n/**\n * Find all .gitignore files from project root (including nested ones).\n * We look at the root .gitignore and any in immediate subdirectories\n * but don't recursively walk the entire tree (too expensive for large repos).\n */\nfunction findGitignoreFiles(projectRoot: string): string[] {\n  const files: string[] = [];\n\n  // Root .gitignore\n  const rootGitignore = join(projectRoot, '.gitignore');\n  if (existsSync(rootGitignore)) {\n    files.push(rootGitignore);\n  }\n\n  // Also check parent directories (for monorepo setups where .gitignore\n  // is at the repo root but the project is in a subdirectory)\n  let dir = dirname(projectRoot);\n  let depth = 0;\n  while (dir !== dirname(dir) && depth < 5) {\n    const parentGitignore = join(dir, '.gitignore');\n    if (existsSync(parentGitignore)) {\n      files.push(parentGitignore);\n    }\n    // Stop if we find a .git directory — that's the repo root\n    if (existsSync(join(dir, '.git'))) break;\n    dir = dirname(dir);\n    depth++;\n  }\n\n  return files;\n}\n\n/**\n * Universal defaults when no .gitignore exists.\n * Covers build artifacts, dependency directories, and virtual environments\n * across all SCIP-supported languages.\n */\nconst DEFAULT_IGNORES = `\n# Dependencies\nnode_modules/\nvendor/\n.bundle/\n\n# Build output\ndist/\nbuild/\nout/\ntarget/\nbin/\nobj/\n\n# Python\n__pycache__/\n*.pyc\n*.pyo\n.venv/\nvenv/\n.env/\nenv/\n*.egg-info/\n\n# Rust\ntarget/\n\n# Java / Kotlin / Scala\n*.class\n.gradle/\n.mvn/\n\n# C# / .NET\nbin/\nobj/\npackages/\n\n# Go\nvendor/\n\n# Dart\n.dart_tool/\nbuild/\n\n# PHP\nvendor/\n\n# IDE / OS\n.idea/\n.vscode/\n*.swp\n*.swo\n.DS_Store\nThumbs.db\n\n# Type definitions (often noise in queries)\n*.d.ts\n`;\n","import { readFileSync, writeFileSync, existsSync, mkdirSync } from 'node:fs';\nimport { join, resolve } from 'node:path';\nimport { createHash } from 'node:crypto';\nimport { homedir } from 'node:os';\nimport type { ProjectConfig, WatchConfig } from './types.js';\n\nconst CONFIG_FILENAME = '.scipquery.json';\n\nconst DEFAULT_WATCH: Required<WatchConfig> = {\n  enabled: false,\n  debounceMs: 30_000,\n  cooldownMs: 60_000,\n  ignore: [],\n};\n\n/**\n * Load project config from .scipquery.json in the project root.\n * Returns defaults for anything not specified.\n */\nexport function loadProjectConfig(projectRoot: string): ProjectConfig {\n  const configPath = join(projectRoot, CONFIG_FILENAME);\n\n  if (!existsSync(configPath)) {\n    return {};\n  }\n\n  try {\n    const raw = readFileSync(configPath, 'utf-8');\n    return JSON.parse(raw) as ProjectConfig;\n  } catch {\n    return {};\n  }\n}\n\n/** Resolve watch config with defaults applied */\nexport function resolveWatchConfig(config: ProjectConfig): Required<WatchConfig> {\n  return {\n    ...DEFAULT_WATCH,\n    ...config.watch,\n  };\n}\n\n/**\n * Resolve the cache directory for a project's SCIP index.\n *\n * Default: ~/.cache/scip-query/projects/<hash>/\n * Override: project config dbPath, or SCIP_QUERY_DB_PATH env var\n *\n * The hash is derived from the absolute project path so each\n * project gets its own isolated index storage.\n */\nexport function resolveCacheDir(projectRoot: string, config?: ProjectConfig): string {\n  // CLI/env override\n  const envOverride = process.env['SCIP_QUERY_CACHE_DIR'];\n  if (envOverride) return ensureDir(envOverride);\n\n  // Project config override\n  if (config?.dbPath) return ensureDir(resolve(projectRoot, config.dbPath));\n\n  // Default: XDG cache dir / fallback to ~/.cache\n  const xdgCache = process.env['XDG_CACHE_HOME'];\n  const cacheBase = xdgCache || join(homedir(), '.cache');\n  const projectHash = createHash('sha256')\n    .update(resolve(projectRoot))\n    .digest('hex')\n    .slice(0, 12);\n\n  const dir = join(cacheBase, 'scip-query', 'projects', projectHash);\n  return ensureDir(dir);\n}\n\n/**\n * Resolve all paths for a project's index files.\n */\nexport function resolveIndexPaths(projectRoot: string, config?: ProjectConfig): {\n  cacheDir: string;\n  dbPath: string;\n  indexPath: string;\n  metaPath: string;\n} {\n  const cacheDir = resolveCacheDir(projectRoot, config);\n  return {\n    cacheDir,\n    dbPath: join(cacheDir, 'index.db'),\n    indexPath: join(cacheDir, 'index.scip'),\n    metaPath: join(cacheDir, 'meta.json'),\n  };\n}\n\n/**\n * Scaffold a default .scipquery.json in the project root.\n * Does not overwrite an existing config.\n */\nexport function initProjectConfig(projectRoot: string, languages: string[]): string {\n  const configPath = join(projectRoot, CONFIG_FILENAME);\n\n  if (existsSync(configPath)) {\n    return configPath;\n  }\n\n  const config: ProjectConfig = {\n    languages: languages as ProjectConfig['languages'],\n    watch: {\n      enabled: false,\n      debounceMs: 30_000,\n      cooldownMs: 60_000,\n    },\n  };\n\n  writeFileSync(configPath, JSON.stringify(config, null, 2) + '\\n');\n  return configPath;\n}\n\nfunction ensureDir(dir: string): string {\n  mkdirSync(dir, { recursive: true });\n  return dir;\n}\n","import { execFileSync } from 'node:child_process';\nimport { existsSync } from 'node:fs';\nimport { join } from 'node:path';\nimport type { SupportedLanguage } from '../types.js';\nimport { detectLanguages } from './detect.js';\nimport { getIndexerConfig } from './indexers.js';\nimport { isBinaryAvailable, isIndexerInstalled, tryInstallIndexer, tryInstallScipCli } from './install.js';\n\nexport interface ReindexOptions {\n  projectRoot: string;\n  /** Override language detection — index only these languages */\n  languages?: SupportedLanguage[];\n  /** Path for the SCIP protobuf output (default: <projectRoot>/index.scip) */\n  outputScip?: string;\n  /** Path for the SQLite output (default: <projectRoot>/index.db) */\n  outputDb?: string;\n  /** Max Node.js heap size in MB (default: 8192) */\n  maxHeapMb?: number;\n  /** Callback for status updates */\n  onStatus?: (message: string) => void;\n  /** Extra flags for pnpm-workspace-aware TS indexing */\n  pnpmWorkspaces?: boolean;\n  /** Skip auto-install prompts */\n  skipAutoInstall?: boolean;\n}\n\nexport interface ReindexResult {\n  languages: SupportedLanguage[];\n  indexPath: string;\n  dbPath: string;\n  durationMs: number;\n}\n\n/**\n * Reindex a project: detect languages, run the appropriate SCIP indexer(s),\n * and convert the output to SQLite.\n */\nexport async function reindex(opts: ReindexOptions): Promise<ReindexResult> {\n  const {\n    projectRoot,\n    maxHeapMb = 8192,\n    onStatus = console.log,\n    skipAutoInstall = false,\n  } = opts;\n\n  const outputScip = opts.outputScip ?? join(projectRoot, 'index.scip');\n  const outputDb = opts.outputDb ?? join(projectRoot, 'index.db');\n  const start = Date.now();\n\n  // Detect or use provided languages\n  const languages = opts.languages ?? detectLanguages(projectRoot);\n  if (languages.length === 0) {\n    throw new Error(\n      'No supported languages detected in this project. ' +\n      'Looked for: tsconfig.json, Cargo.toml, go.mod, pyproject.toml, etc.',\n    );\n  }\n\n  onStatus(`Detected languages: ${languages.join(', ')}`);\n\n  // Check that the scip CLI is available, auto-install if needed\n  if (!isBinaryAvailable('scip')) {\n    if (skipAutoInstall) {\n      throw new Error(\n        'The scip CLI is required but not found on PATH.\\n' +\n        'Install from: https://github.com/sourcegraph/scip/releases',\n      );\n    }\n    onStatus('scip CLI not found on PATH. Attempting auto-install...');\n    if (!tryInstallScipCli(onStatus)) {\n      throw new Error(\n        'The scip CLI is required but could not be installed.\\n' +\n        'Install manually from: https://github.com/sourcegraph/scip/releases',\n      );\n    }\n  }\n\n  const env = {\n    ...process.env,\n    NODE_OPTIONS: `--max-old-space-size=${maxHeapMb}`,\n  };\n\n  // Index each language\n  for (const lang of languages) {\n    const config = getIndexerConfig(lang);\n\n    // Check if indexer is installed, auto-install if needed\n    if (!isIndexerInstalled(config)) {\n      if (skipAutoInstall) {\n        throw new Error(\n          `${config.indexerBinary} is required to index ${lang} but not found on PATH.\\n` +\n          (config.installUrl ? `Install from: ${config.installUrl}` : `Make sure ${config.indexerBinary} is installed and available on PATH.`),\n        );\n      }\n      onStatus(`${config.indexerBinary} not found. Attempting auto-install...`);\n      if (!tryInstallIndexer(config, onStatus)) {\n        throw new Error(\n          `${config.indexerBinary} is required to index ${lang} but could not be installed.\\n` +\n          (config.installUrl ? `Install manually from: ${config.installUrl}` : `Make sure ${config.indexerBinary} is installed and available on PATH.`),\n        );\n      }\n    }\n\n    onStatus(`Indexing ${lang} with ${config.indexerBinary}...`);\n\n    const { binary, args } = config.indexArgs({\n      projectRoot,\n      outputPath: outputScip,\n      pnpmWorkspaces: opts.pnpmWorkspaces,\n    });\n\n    try {\n      execFileSync(binary, args, {\n        cwd: projectRoot,\n        env,\n        stdio: 'pipe',\n        maxBuffer: 50 * 1024 * 1024,\n      });\n    } catch (err) {\n      const msg = err instanceof Error ? err.message : String(err);\n      throw new Error(\n        `Failed to index ${lang} with ${config.indexerBinary}: ${msg}\\n` +\n        `Make sure ${config.indexerBinary} is installed and available on PATH.`,\n      );\n    }\n  }\n\n  // Convert SCIP protobuf to SQLite\n  onStatus('Converting to SQLite...');\n  if (!existsSync(outputScip)) {\n    throw new Error(`SCIP index not found at ${outputScip} after indexing`);\n  }\n\n  try {\n    execFileSync('scip', ['expt-convert', '--output', outputDb, outputScip], {\n      env,\n      stdio: 'pipe',\n      maxBuffer: 50 * 1024 * 1024,\n    });\n  } catch (err) {\n    const msg = err instanceof Error ? err.message : String(err);\n    throw new Error(`Failed to convert SCIP index to SQLite: ${msg}`);\n  }\n\n  const durationMs = Date.now() - start;\n  onStatus(`Done in ${(durationMs / 1000).toFixed(1)}s`);\n\n  return { languages, indexPath: outputScip, dbPath: outputDb, durationMs };\n}\n\nexport { detectLanguages } from './detect.js';\nexport { getIndexerConfig, INDEXER_CONFIGS } from './indexers.js';\nexport { isBinaryAvailable, isIndexerInstalled, tryInstallIndexer, tryInstallScipCli } from './install.js';\n","import { existsSync } from 'node:fs';\nimport { join } from 'node:path';\nimport type { SupportedLanguage } from '../types.js';\n\ninterface LanguageMarker {\n  language: SupportedLanguage;\n  files: string[];\n}\n\n/**\n * Marker files that indicate a language is present in a project.\n * Ordered roughly by specificity — more specific markers first.\n */\nconst LANGUAGE_MARKERS: LanguageMarker[] = [\n  { language: 'typescript', files: ['tsconfig.json', 'tsconfig.base.json'] },\n  { language: 'rust', files: ['Cargo.toml'] },\n  { language: 'go', files: ['go.mod'] },\n  { language: 'java', files: ['pom.xml', 'build.gradle', 'build.gradle.kts'] },\n  { language: 'kotlin', files: ['build.gradle.kts'] },\n  { language: 'scala', files: ['build.sbt'] },\n  { language: 'python', files: ['pyproject.toml', 'setup.py', 'setup.cfg', 'Pipfile'] },\n  { language: 'ruby', files: ['Gemfile'] },\n  { language: 'csharp', files: ['*.csproj', '*.sln'] },\n  { language: 'dart', files: ['pubspec.yaml'] },\n  { language: 'php', files: ['composer.json'] },\n  { language: 'javascript', files: ['package.json'] }, // Last — very common, low specificity\n];\n\n/**\n * Detect which languages are present in a project directory\n * by checking for marker files.\n */\nexport function detectLanguages(projectRoot: string): SupportedLanguage[] {\n  const detected: SupportedLanguage[] = [];\n\n  for (const marker of LANGUAGE_MARKERS) {\n    for (const file of marker.files) {\n      if (file.includes('*')) {\n        // Glob patterns — skip for now, basic detection only\n        continue;\n      }\n      if (existsSync(join(projectRoot, file))) {\n        if (!detected.includes(marker.language)) {\n          detected.push(marker.language);\n        }\n        break;\n      }\n    }\n  }\n\n  // If we found TypeScript, don't also report JavaScript (it's implied)\n  if (detected.includes('typescript')) {\n    const jsIdx = detected.indexOf('javascript');\n    if (jsIdx !== -1) detected.splice(jsIdx, 1);\n  }\n\n  return detected;\n}\n","import type { SupportedLanguage, IndexerConfig } from '../types.js';\n\n/**\n * Indexer configurations for each supported language.\n * Each entry describes how to produce a SCIP index for that language.\n *\n * The `scip` CLI binary is required for all languages (to convert protobuf -> SQLite).\n * Each language also needs its own SCIP indexer installed.\n */\nexport const INDEXER_CONFIGS: Record<SupportedLanguage, IndexerConfig> = {\n  typescript: {\n    language: 'typescript',\n    indexerBinary: 'scip-typescript',\n    checkCommand: 'npx scip-typescript --version',\n    indexArgs: ({ outputPath, pnpmWorkspaces }) => {\n      const args = ['scip-typescript', 'index', '--infer-tsconfig', '--output', outputPath, '--no-progress-bar'];\n      if (pnpmWorkspaces) args.splice(2, 0, '--pnpm-workspaces');\n      return { binary: 'npx', args };\n    },\n    markerFiles: ['tsconfig.json'],\n    installMethods: [\n      { label: 'npm', prerequisite: 'npm', binary: 'npm', args: ['install', '-g', '@sourcegraph/scip-typescript'] },\n    ],\n    installUrl: 'https://github.com/sourcegraph/scip-typescript',\n  },\n\n  javascript: {\n    language: 'javascript',\n    indexerBinary: 'scip-typescript',\n    checkCommand: 'npx scip-typescript --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'npx',\n      args: ['scip-typescript', 'index', '--infer-tsconfig', '--output', outputPath, '--no-progress-bar'],\n    }),\n    markerFiles: ['package.json'],\n    installMethods: [\n      { label: 'npm', prerequisite: 'npm', binary: 'npm', args: ['install', '-g', '@sourcegraph/scip-typescript'] },\n    ],\n    installUrl: 'https://github.com/sourcegraph/scip-typescript',\n  },\n\n  java: {\n    language: 'java',\n    indexerBinary: 'scip-java',\n    checkCommand: 'scip-java --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-java',\n      args: ['index', '--output', outputPath],\n    }),\n    markerFiles: ['pom.xml', 'build.gradle'],\n    installMethods: [\n      { label: 'coursier', prerequisite: 'cs', binary: 'cs', args: ['install', 'scip-java'] },\n    ],\n    installUrl: 'https://github.com/sourcegraph/scip-java/releases',\n  },\n\n  scala: {\n    language: 'scala',\n    indexerBinary: 'scip-java',\n    checkCommand: 'scip-java --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-java',\n      args: ['index', '--output', outputPath],\n    }),\n    markerFiles: ['build.sbt'],\n    installMethods: [\n      { label: 'coursier', prerequisite: 'cs', binary: 'cs', args: ['install', 'scip-java'] },\n    ],\n    installUrl: 'https://github.com/sourcegraph/scip-java/releases',\n  },\n\n  kotlin: {\n    language: 'kotlin',\n    indexerBinary: 'scip-java',\n    checkCommand: 'scip-java --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-java',\n      args: ['index', '--output', outputPath],\n    }),\n    markerFiles: ['build.gradle.kts'],\n    installMethods: [\n      { label: 'coursier', prerequisite: 'cs', binary: 'cs', args: ['install', 'scip-java'] },\n    ],\n    installUrl: 'https://github.com/sourcegraph/scip-java/releases',\n  },\n\n  rust: {\n    language: 'rust',\n    indexerBinary: 'rust-analyzer',\n    checkCommand: 'rust-analyzer --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'rust-analyzer',\n      args: ['scip', '.', '--output', outputPath],\n    }),\n    markerFiles: ['Cargo.toml'],\n    installMethods: [\n      { label: 'rustup', prerequisite: 'rustup', binary: 'rustup', args: ['component', 'add', 'rust-analyzer'] },\n    ],\n    installUrl: 'https://github.com/rust-lang/rust-analyzer',\n  },\n\n  python: {\n    language: 'python',\n    indexerBinary: 'scip-python',\n    checkCommand: 'scip-python --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-python',\n      args: ['index', '--output', outputPath, '--project-name', 'project'],\n    }),\n    markerFiles: ['pyproject.toml', 'setup.py'],\n    installMethods: [\n      { label: 'npm', prerequisite: 'npm', binary: 'npm', args: ['install', '-g', 'scip-python-plus'] },\n    ],\n    installUrl: 'https://github.com/PlunderStruck/scip-python',\n  },\n\n  ruby: {\n    language: 'ruby',\n    indexerBinary: 'scip-ruby',\n    checkCommand: 'scip-ruby --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-ruby',\n      args: ['--output', outputPath],\n    }),\n    markerFiles: ['Gemfile'],\n    installMethods: [],\n    installUrl: 'https://github.com/sourcegraph/scip-ruby/releases',\n  },\n\n  go: {\n    language: 'go',\n    indexerBinary: 'scip-go',\n    checkCommand: 'scip-go --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-go',\n      args: ['--output', outputPath],\n    }),\n    markerFiles: ['go.mod'],\n    installMethods: [\n      { label: 'go install', prerequisite: 'go', binary: 'go', args: ['install', 'github.com/sourcegraph/scip-go@latest'] },\n    ],\n    installUrl: 'https://github.com/sourcegraph/scip-go',\n  },\n\n  cpp: {\n    language: 'cpp',\n    indexerBinary: 'scip-clang',\n    checkCommand: 'scip-clang --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-clang',\n      args: ['--output', outputPath],\n    }),\n    markerFiles: ['CMakeLists.txt', 'Makefile'],\n    installMethods: [],\n    installUrl: 'https://github.com/sourcegraph/scip-clang/releases',\n  },\n\n  c: {\n    language: 'c',\n    indexerBinary: 'scip-clang',\n    checkCommand: 'scip-clang --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-clang',\n      args: ['--output', outputPath],\n    }),\n    markerFiles: ['CMakeLists.txt', 'Makefile'],\n    installMethods: [],\n    installUrl: 'https://github.com/sourcegraph/scip-clang/releases',\n  },\n\n  csharp: {\n    language: 'csharp',\n    indexerBinary: 'scip-dotnet',\n    checkCommand: 'scip-dotnet --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-dotnet',\n      args: ['index', '--output', outputPath],\n    }),\n    markerFiles: [],\n    installMethods: [\n      { label: 'dotnet', prerequisite: 'dotnet', binary: 'dotnet', args: ['tool', 'install', '--global', 'scip-dotnet'] },\n    ],\n    installUrl: 'https://github.com/sourcegraph/scip-dotnet/releases',\n  },\n\n  dart: {\n    language: 'dart',\n    indexerBinary: 'scip-dart',\n    checkCommand: 'scip-dart --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-dart',\n      args: ['index', '--output', outputPath],\n    }),\n    markerFiles: ['pubspec.yaml'],\n    installMethods: [\n      { label: 'dart pub', prerequisite: 'dart', binary: 'dart', args: ['pub', 'global', 'activate', 'scip_dart'] },\n    ],\n    installUrl: 'https://github.com/Workiva/scip-dart/releases',\n  },\n\n  php: {\n    language: 'php',\n    indexerBinary: 'scip-php',\n    checkCommand: 'scip-php --version',\n    indexArgs: ({ outputPath }) => ({\n      binary: 'scip-php',\n      args: ['index', '--output', outputPath],\n    }),\n    markerFiles: ['composer.json'],\n    installMethods: [\n      { label: 'composer', prerequisite: 'composer', binary: 'composer', args: ['global', 'require', 'davidrjenni/scip-php'] },\n    ],\n    installUrl: 'https://github.com/davidrjenni/scip-php/releases',\n  },\n};\n\n/** Get the indexer config for a language */\nexport function getIndexerConfig(language: SupportedLanguage): IndexerConfig {\n  return INDEXER_CONFIGS[language];\n}\n","import { execFileSync } from 'node:child_process';\nimport { platform } from 'node:os';\nimport type { IndexerConfig } from '../types.js';\n\nconst IS_WINDOWS = platform() === 'win32';\n\n/**\n * Check if a binary is available on PATH.\n */\nexport function isBinaryAvailable(name: string): boolean {\n  const cmd = IS_WINDOWS ? 'where' : 'which';\n  try {\n    execFileSync(cmd, [name], { stdio: 'pipe' });\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Check if an indexer's binary is available on PATH.\n */\nexport function isIndexerInstalled(config: IndexerConfig): boolean {\n  return isBinaryAvailable(config.indexerBinary);\n}\n\n/**\n * Attempt to auto-install an indexer using its configured install methods.\n * Tries each method in order, checking prerequisites first.\n * Returns true if installation succeeded.\n */\nexport function tryInstallIndexer(\n  config: IndexerConfig,\n  onStatus: (msg: string) => void,\n): boolean {\n  const methods = config.installMethods;\n  if (!methods?.length) {\n    onStatus(`No auto-install method available for ${config.indexerBinary}.`);\n    if (config.installUrl) {\n      onStatus(`Install manually from: ${config.installUrl}`);\n    }\n    return false;\n  }\n\n  for (const method of methods) {\n    if (!isBinaryAvailable(method.prerequisite)) {\n      continue;\n    }\n\n    onStatus(`Installing ${config.indexerBinary} via ${method.label}...`);\n    try {\n      execFileSync(method.binary, method.args, {\n        stdio: 'inherit',\n        timeout: 300_000,\n        env: process.env,\n      });\n\n      if (isIndexerInstalled(config)) {\n        onStatus(`Successfully installed ${config.indexerBinary} via ${method.label}`);\n        return true;\n      }\n      onStatus(`${method.label} command completed but ${config.indexerBinary} not found on PATH`);\n    } catch (err) {\n      const msg = err instanceof Error ? err.message : String(err);\n      onStatus(`${method.label} install failed: ${msg}`);\n    }\n  }\n\n  onStatus(`Could not auto-install ${config.indexerBinary}.`);\n  if (config.installUrl) {\n    onStatus(`Install manually from: ${config.installUrl}`);\n  }\n  return false;\n}\n\n/**\n * Attempt to auto-install the `scip` CLI binary.\n * Tries brew (macOS), then go install, then prints manual instructions.\n * Returns true if installation succeeded.\n */\nexport function tryInstallScipCli(\n  onStatus: (msg: string) => void,\n): boolean {\n  // macOS: try Homebrew first\n  if (platform() === 'darwin' && isBinaryAvailable('brew')) {\n    onStatus('Installing scip CLI via Homebrew...');\n    try {\n      execFileSync('brew', ['install', 'sourcegraph/scip/scip'], {\n        stdio: 'inherit',\n        timeout: 300_000,\n        env: process.env,\n      });\n      if (isBinaryAvailable('scip')) {\n        onStatus('Successfully installed scip CLI via Homebrew');\n        return true;\n      }\n    } catch (err) {\n      const msg = err instanceof Error ? err.message : String(err);\n      onStatus(`Homebrew install failed: ${msg}`);\n    }\n  }\n\n  // Any platform: try go install\n  if (isBinaryAvailable('go')) {\n    onStatus('Installing scip CLI via go install...');\n    try {\n      execFileSync('go', ['install', 'github.com/sourcegraph/scip/cmd/scip@latest'], {\n        stdio: 'inherit',\n        timeout: 300_000,\n        env: process.env,\n      });\n      if (isBinaryAvailable('scip')) {\n        onStatus('Successfully installed scip CLI via go install');\n        return true;\n      }\n    } catch (err) {\n      const msg = err instanceof Error ? err.message : String(err);\n      onStatus(`go install failed: ${msg}`);\n    }\n  }\n\n  onStatus('Could not auto-install scip CLI.');\n  onStatus('Install manually from: https://github.com/sourcegraph/scip/releases');\n  return false;\n}\n","import { watch } from 'node:fs';\nimport { readFileSync, existsSync, renameSync } from 'node:fs';\nimport { join, relative } from 'node:path';\nimport { fork } from 'node:child_process';\nimport ignore from 'ignore';\nimport type { WatcherStatus, ProjectConfig, SupportedLanguage } from './types.js';\nimport { resolveWatchConfig, resolveIndexPaths } from './config.js';\nimport { createGitignoreFilter } from './gitignore-filter.js';\n\nexport interface WatcherOptions {\n  projectRoot: string;\n  config: ProjectConfig;\n  languages?: SupportedLanguage[];\n  onStatus?: (status: WatcherStatus) => void;\n  onReindexComplete?: (durationMs: number) => void;\n  onError?: (error: Error) => void;\n}\n\n/**\n * File watcher that triggers single-flight background reindexing.\n *\n * Design:\n *  - Debounce: waits 30s (configurable) after the last file change\n *  - Single-flight: only one reindex runs at a time, never queued\n *  - Dirty flag: changes during reindex schedule ONE follow-up\n *  - Cooldown: minimum interval between reindex completions\n *  - Atomic swap: writes to index.db.tmp, renames on success\n */\nexport class Watcher {\n  private projectRoot: string;\n  private watchConfig: Required<NonNullable<ProjectConfig['watch']>>;\n  private indexPaths: ReturnType<typeof resolveIndexPaths>;\n  private languages?: SupportedLanguage[];\n  private pnpmWorkspaces: boolean;\n\n  private onStatus: (status: WatcherStatus) => void;\n  private onReindexComplete: (durationMs: number) => void;\n  private onError: (error: Error) => void;\n\n  // State machine\n  private status: WatcherStatus = { state: 'idle' };\n  private debounceTimer: ReturnType<typeof setTimeout> | null = null;\n  private cooldownTimer: ReturnType<typeof setTimeout> | null = null;\n  private dirty = false;\n  private changedFiles = 0;\n  private reindexInFlight = false;\n  private lastReindexEnd = 0;\n\n  // fs.watch watchers (one per watched directory)\n  private fsWatchers: ReturnType<typeof watch>[] = [];\n  private gitignoreFilter: ReturnType<typeof createGitignoreFilter>;\n  private extraIgnore: ReturnType<typeof ignore>;\n  private stopped = false;\n\n  constructor(opts: WatcherOptions) {\n    this.projectRoot = opts.projectRoot;\n    this.watchConfig = resolveWatchConfig(opts.config);\n    this.indexPaths = resolveIndexPaths(opts.projectRoot, opts.config);\n    this.languages = opts.languages;\n    this.pnpmWorkspaces = opts.config.indexer?.typescript?.pnpmWorkspaces ?? false;\n\n    this.onStatus = opts.onStatus ?? (() => {});\n    this.onReindexComplete = opts.onReindexComplete ?? (() => {});\n    this.onError = opts.onError ?? ((e) => console.error(e.message));\n\n    this.gitignoreFilter = createGitignoreFilter(opts.projectRoot);\n    this.extraIgnore = ignore();\n    if (this.watchConfig.ignore.length > 0) {\n      this.extraIgnore.add(this.watchConfig.ignore);\n    }\n  }\n\n  /** Start watching for file changes */\n  start(): void {\n    this.stopped = false;\n    this.setStatus({ state: 'idle' });\n\n    // Use recursive fs.watch on the project root\n    // This is supported on macOS (FSEvents) and Windows\n    // On Linux, falls back to inotify (may need per-directory watchers for large trees)\n    try {\n      const watcher = watch(\n        this.projectRoot,\n        { recursive: true },\n        (_event, filename) => {\n          if (filename && !this.stopped) {\n            this.handleFileChange(filename);\n          }\n        },\n      );\n      this.fsWatchers.push(watcher);\n    } catch {\n      this.onError(new Error(\n        'Failed to start file watcher. On Linux, you may need to increase inotify limits: ' +\n        'sysctl -w fs.inotify.max_user_watches=524288',\n      ));\n    }\n  }\n\n  /** Stop watching and clean up */\n  stop(): void {\n    this.stopped = true;\n    for (const w of this.fsWatchers) w.close();\n    this.fsWatchers = [];\n    if (this.debounceTimer) clearTimeout(this.debounceTimer);\n    if (this.cooldownTimer) clearTimeout(this.cooldownTimer);\n    this.setStatus({ state: 'idle' });\n  }\n\n  /** Get current watcher status */\n  getStatus(): WatcherStatus {\n    return this.status;\n  }\n\n  // ── Internal ─────────────────────────────────────────────\n\n  private handleFileChange(filename: string): void {\n    // Filter: skip gitignored files and extra ignore patterns\n    const rel = relative(this.projectRoot, join(this.projectRoot, filename));\n    if (this.gitignoreFilter.isIgnored(rel)) return;\n    if (this.extraIgnore.ignores(rel)) return;\n\n    // Skip the index files themselves\n    if (filename.endsWith('index.db') || filename.endsWith('index.scip') ||\n        filename.endsWith('index.db.tmp') || filename.endsWith('.scipquery.json')) {\n      return;\n    }\n\n    this.changedFiles++;\n\n    if (this.reindexInFlight) {\n      // Reindex is running — just mark dirty, don't schedule anything\n      this.dirty = true;\n      this.setStatus({\n        state: 'indexing',\n        startedAt: (this.status as { startedAt: number }).startedAt,\n      });\n      return;\n    }\n\n    if (this.status.state === 'cooldown') {\n      // In cooldown — mark dirty, the cooldown handler will pick it up\n      this.dirty = true;\n      this.setStatus({ state: 'cooldown', until: (this.status as { until: number }).until, dirty: true });\n      return;\n    }\n\n    // Reset the debounce timer — every new change pushes the trigger out\n    if (this.debounceTimer) clearTimeout(this.debounceTimer);\n\n    const reindexAt = Date.now() + this.watchConfig.debounceMs;\n    this.setStatus({ state: 'waiting', changedFiles: this.changedFiles, reindexAt });\n\n    this.debounceTimer = setTimeout(() => {\n      this.debounceTimer = null;\n      this.triggerReindex();\n    }, this.watchConfig.debounceMs);\n  }\n\n  private triggerReindex(): void {\n    if (this.reindexInFlight || this.stopped) return;\n\n    // Check cooldown\n    const timeSinceLastReindex = Date.now() - this.lastReindexEnd;\n    if (this.lastReindexEnd > 0 && timeSinceLastReindex < this.watchConfig.cooldownMs) {\n      const remaining = this.watchConfig.cooldownMs - timeSinceLastReindex;\n      this.dirty = true;\n      const until = Date.now() + remaining;\n      this.setStatus({ state: 'cooldown', until, dirty: true });\n\n      this.cooldownTimer = setTimeout(() => {\n        this.cooldownTimer = null;\n        if (this.dirty && !this.stopped) {\n          this.dirty = false;\n          this.triggerReindex();\n        }\n      }, remaining);\n      return;\n    }\n\n    this.reindexInFlight = true;\n    this.dirty = false;\n    this.changedFiles = 0;\n    const startedAt = Date.now();\n    this.setStatus({ state: 'indexing', startedAt });\n\n    // Run reindex in a child process so it doesn't block the watcher\n    this.runReindex()\n      .then((durationMs) => {\n        this.reindexInFlight = false;\n        this.lastReindexEnd = Date.now();\n        this.onReindexComplete(durationMs);\n\n        if (this.dirty && !this.stopped) {\n          // Changes arrived during reindex — enter cooldown then reindex again\n          const until = Date.now() + this.watchConfig.cooldownMs;\n          this.setStatus({ state: 'cooldown', until, dirty: true });\n\n          this.cooldownTimer = setTimeout(() => {\n            this.cooldownTimer = null;\n            if (this.dirty && !this.stopped) {\n              this.dirty = false;\n              this.triggerReindex();\n            } else {\n              this.setStatus({ state: 'idle' });\n            }\n          }, this.watchConfig.cooldownMs);\n        } else {\n          this.setStatus({ state: 'idle' });\n        }\n      })\n      .catch((err) => {\n        this.reindexInFlight = false;\n        this.lastReindexEnd = Date.now();\n        this.onError(err instanceof Error ? err : new Error(String(err)));\n        this.setStatus({ state: 'idle' });\n      });\n  }\n\n  /**\n   * Run the reindex in a forked child process.\n   * Writes to index.db.tmp, then atomically renames to index.db.\n   */\n  private runReindex(): Promise<number> {\n    return new Promise((resolve, reject) => {\n      const start = Date.now();\n      const tmpDb = this.indexPaths.dbPath + '.tmp';\n      const tmpScip = this.indexPaths.indexPath + '.tmp';\n\n      // Fork a child that runs the reindex\n      const child = fork(\n        new URL('./reindex-worker.js', import.meta.url).pathname,\n        [],\n        {\n          env: {\n            ...process.env,\n            SCIP_REINDEX_PROJECT_ROOT: this.projectRoot,\n            SCIP_REINDEX_OUTPUT_SCIP: tmpScip,\n            SCIP_REINDEX_OUTPUT_DB: tmpDb,\n            SCIP_REINDEX_LANGUAGES: this.languages?.join(',') ?? '',\n            SCIP_REINDEX_PNPM_WORKSPACES: this.pnpmWorkspaces ? '1' : '',\n          },\n          stdio: 'pipe',\n        },\n      );\n\n      child.on('exit', (code) => {\n        if (code === 0) {\n          // Atomic swap\n          try {\n            if (existsSync(tmpDb)) {\n              renameSync(tmpDb, this.indexPaths.dbPath);\n            }\n            if (existsSync(tmpScip)) {\n              renameSync(tmpScip, this.indexPaths.indexPath);\n            }\n            resolve(Date.now() - start);\n          } catch (err) {\n            reject(new Error(`Atomic swap failed: ${err}`));\n          }\n        } else {\n          reject(new Error(`Reindex worker exited with code ${code}`));\n        }\n      });\n\n      child.on('error', reject);\n    });\n  }\n\n  private setStatus(status: WatcherStatus): void {\n    this.status = status;\n    this.onStatus(status);\n  }\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { StatsResult } from '../types.js';\n\nexport function stats(db: ScipDatabase): StatsResult {\n  const documents = db.get<{ c: number }>('SELECT COUNT(*) as c FROM documents')!.c;\n  const symbols = db.get<{ c: number }>('SELECT COUNT(*) as c FROM global_symbols')!.c;\n  const definitions = db.get<{ c: number }>(\n    'SELECT COUNT(*) as c FROM mentions WHERE role = 1',\n  )!.c;\n  const references = db.get<{ c: number }>(\n    'SELECT COUNT(*) as c FROM mentions WHERE role = 0',\n  )!.c;\n\n  return {\n    documents,\n    symbols,\n    definitions,\n    references,\n    indexSizeBytes: db.sizeBytes(),\n    lastBuilt: db.lastModified(),\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { FileResult } from '../types.js';\n\nexport function files(db: ScipDatabase, pattern: string): FileResult[] {\n  const rows = db.all<{ relative_path: string }>(\n    `SELECT relative_path FROM documents\n     WHERE relative_path LIKE ?\n     ORDER BY relative_path`,\n    `%${pattern}%`,\n  );\n\n  // Apply gitignore filtering\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({ relativePath: r.relative_path }));\n}\n","import type { ScipSymbol, ScipDescriptor, ScipLocalSymbol, DescriptorSuffix } from './types.js';\n\n/**\n * SCIP Symbol Grammar (from the SCIP spec):\n *\n *   <symbol>     ::= <scheme> ' ' <package> ' ' <descriptor>+ | 'local ' <local-id>\n *   <package>    ::= <manager> ' ' <package-name> ' ' <version> ' '\n *   <descriptor> ::= <name> <suffix>\n *\n * Suffix characters:\n *   /    namespace\n *   #    type (class, interface, enum)\n *   .    term (variable, field, property)\n *   ().  method\n *   [    type parameter\n *   ()   parameter\n *   :    meta\n *   !    macro\n *\n * Names may be backtick-escaped: `some.weird/name`\n */\n\nconst SUFFIX_MAP: Record<string, DescriptorSuffix> = {\n  '/': 'namespace',\n  '#': 'type',\n  '.': 'term',\n  '[': 'type-param',\n  ':': 'meta',\n  '!': 'macro',\n};\n\n/**\n * Parse a SCIP symbol string into its structured components.\n * Works for any SCIP-indexed language (TypeScript, Java, Rust, Python, etc.)\n */\nexport function parseSymbol(raw: string): ScipSymbol | ScipLocalSymbol {\n  if (raw.startsWith('local ')) {\n    return { kind: 'local', id: raw.slice(6), raw };\n  }\n\n  // Split: <scheme> <manager> <package-name> <version> <descriptors...>\n  // The tricky part: package-name can contain spaces if backtick-escaped\n  const parts = raw.split(' ');\n  if (parts.length < 4) {\n    // Malformed — return a best-effort parse\n    return {\n      scheme: parts[0] ?? '',\n      manager: parts[1] ?? '',\n      packageName: parts[2] ?? '',\n      version: '',\n      descriptors: [],\n      raw,\n    };\n  }\n\n  const scheme = parts[0]!;\n  const manager = parts[1]!;\n\n  // Package name and version: package name might be backtick-escaped\n  // After scheme + manager, we need to find package + version + descriptor string\n  let restAfterManager = raw.slice(scheme.length + 1 + manager.length + 1);\n\n  // Parse package name (may be backtick-escaped)\n  let packageName: string;\n  if (restAfterManager.startsWith('`')) {\n    const closingTick = restAfterManager.indexOf('`', 1);\n    if (closingTick === -1) {\n      packageName = restAfterManager.slice(1);\n      restAfterManager = '';\n    } else {\n      packageName = restAfterManager.slice(1, closingTick);\n      restAfterManager = restAfterManager.slice(closingTick + 2); // skip ` and space\n    }\n  } else {\n    const spaceIdx = restAfterManager.indexOf(' ');\n    if (spaceIdx === -1) {\n      packageName = restAfterManager;\n      restAfterManager = '';\n    } else {\n      packageName = restAfterManager.slice(0, spaceIdx);\n      restAfterManager = restAfterManager.slice(spaceIdx + 1);\n    }\n  }\n\n  // Parse version\n  let version: string;\n  const versionSpaceIdx = restAfterManager.indexOf(' ');\n  if (versionSpaceIdx === -1) {\n    version = restAfterManager;\n    restAfterManager = '';\n  } else {\n    version = restAfterManager.slice(0, versionSpaceIdx);\n    restAfterManager = restAfterManager.slice(versionSpaceIdx + 1);\n  }\n\n  // Parse descriptors from the remaining string\n  const descriptors = parseDescriptors(restAfterManager);\n\n  return { scheme, manager, packageName, version, descriptors, raw };\n}\n\n/**\n * Parse the descriptor chain from a SCIP symbol.\n *\n * SCIP descriptor grammar:\n *   namespace:   name/\n *   type:        name#\n *   term:        name.\n *   method:      name(disambiguator).\n *   type-param:  [name]          (bracket-wrapped, prefix syntax)\n *   parameter:   (name)          (paren-wrapped, prefix syntax)\n *   meta:        name:\n *   macro:       name!\n *\n * Names can be backtick-escaped: `some/name.with.dots`\n */\nfunction parseDescriptors(input: string): ScipDescriptor[] {\n  const descriptors: ScipDescriptor[] = [];\n  let i = 0;\n\n  while (i < input.length) {\n    // Type parameter: [name]\n    if (input[i] === '[') {\n      const closeBracket = input.indexOf(']', i + 1);\n      if (closeBracket === -1) {\n        descriptors.push({ name: input.slice(i + 1), suffix: 'type-param' });\n        break;\n      }\n      descriptors.push({ name: input.slice(i + 1, closeBracket), suffix: 'type-param' });\n      i = closeBracket + 1;\n      continue;\n    }\n\n    // Parameter: (name) — only when ( appears at descriptor start with no preceding name\n    if (input[i] === '(' && (descriptors.length === 0 || i === 0 || isSuffixChar(input[i - 1]!))) {\n      const closeParen = input.indexOf(')', i + 1);\n      if (closeParen !== -1 && input[closeParen + 1] !== '.') {\n        // This is a parameter (name), not a method disambiguator\n        descriptors.push({ name: input.slice(i + 1, closeParen), suffix: 'parameter' });\n        i = closeParen + 1;\n        continue;\n      }\n    }\n\n    let name: string;\n\n    // Backtick-escaped name\n    if (input[i] === '`') {\n      const closingTick = input.indexOf('`', i + 1);\n      if (closingTick === -1) {\n        name = input.slice(i + 1);\n        i = input.length;\n        descriptors.push({ name, suffix: 'term' });\n        break;\n      }\n      name = input.slice(i + 1, closingTick);\n      i = closingTick + 1;\n    } else {\n      // Read name until we hit a suffix character\n      const start = i;\n      while (i < input.length && !isSuffixChar(input[i]!)) {\n        i++;\n      }\n      name = input.slice(start, i);\n    }\n\n    // Parse suffix after name\n    if (i >= input.length) {\n      if (name) descriptors.push({ name, suffix: 'term' });\n      break;\n    }\n\n    const char = input[i]!;\n\n    // Method: name(disambiguator).\n    if (char === '(') {\n      const closeParen = input.indexOf(')', i + 1);\n      if (closeParen !== -1 && input[closeParen + 1] === '.') {\n        descriptors.push({ name, suffix: 'method' });\n        i = closeParen + 2; // skip past ).\n      } else if (closeParen !== -1) {\n        // Bare (disambiguator) without . — treat as method anyway (common in practice)\n        descriptors.push({ name, suffix: 'method' });\n        i = closeParen + 1;\n      } else {\n        descriptors.push({ name, suffix: 'term' });\n        i++;\n      }\n    } else {\n      const suffix = SUFFIX_MAP[char];\n      if (suffix) {\n        descriptors.push({ name, suffix });\n        i += 1;\n      } else {\n        i += 1; // Unknown suffix — skip\n      }\n    }\n  }\n\n  return descriptors;\n}\n\nfunction isSuffixChar(c: string): boolean {\n  return c === '/' || c === '#' || c === '.' || c === '(' || c === '[' || c === ':' || c === '!';\n}\n\n/**\n * Convert a parsed SCIP symbol to a short, human-readable name.\n * Language-agnostic: works for any SCIP-indexed language.\n *\n * Examples:\n *   \"scip-typescript npm @vega/api 0.1.3 src/modules/auth/auth.service.ts/AuthService#login().\"\n *   → \"auth.service:AuthService:login()\"\n *\n *   \"scip-java maven com.example/mylib 1.0.0 com/example/MyClass#doStuff().\"\n *   → \"MyClass:doStuff()\"\n *\n *   \"rust-analyzer cargo my-crate 0.1.0 src/lib.rs/MyStruct#new().\"\n *   → \"lib:MyStruct:new()\"\n */\nexport function shortenSymbol(raw: string): string {\n  const parsed = parseSymbol(raw);\n  if ('kind' in parsed && parsed.kind === 'local') {\n    return `local:${parsed.id}`;\n  }\n\n  const sym = parsed as ScipSymbol;\n  if (sym.descriptors.length === 0) return sym.raw;\n\n  const parts: string[] = [];\n  for (const desc of sym.descriptors) {\n    // Strip file extensions from namespace descriptors (the file path parts)\n    let name = desc.name;\n    if (desc.suffix === 'namespace') {\n      // Remove common file extensions\n      name = name\n        .replace(/\\.(ts|tsx|js|jsx|mjs|cjs)$/, '')\n        .replace(/\\.(py|pyi)$/, '')\n        .replace(/\\.(rs)$/, '')\n        .replace(/\\.(java|scala|kt|kts)$/, '')\n        .replace(/\\.(rb)$/, '')\n        .replace(/\\.(go)$/, '')\n        .replace(/\\.(cs|vb)$/, '')\n        .replace(/\\.(dart)$/, '')\n        .replace(/\\.(php)$/, '')\n        .replace(/\\.(c|cc|cpp|cxx|h|hpp)$/, '');\n    }\n\n    // Skip empty names (can happen with trailing suffixes)\n    if (!name) continue;\n\n    // For methods, append () for clarity\n    if (desc.suffix === 'method') {\n      parts.push(`${name}()`);\n    } else {\n      parts.push(name);\n    }\n  }\n\n  return parts.join(':');\n}\n\n/**\n * Extract just the leaf name from a SCIP symbol.\n * Useful when you only need the function/class/variable name without path context.\n */\nexport function leafName(raw: string): string {\n  const parsed = parseSymbol(raw);\n  if ('kind' in parsed && parsed.kind === 'local') {\n    return parsed.id;\n  }\n\n  const sym = parsed as ScipSymbol;\n  if (sym.descriptors.length === 0) return '';\n\n  const last = sym.descriptors[sym.descriptors.length - 1]!;\n  return last.name;\n}\n","/**\n * Clean up the raw doc/signature string from the SCIP index.\n *\n * Shared across symbols, trace, and system queries.\n * Previously duplicated as cleanSig/cleanSignature in three files.\n */\nexport function cleanSignature(sig: string | null): string | null {\n  if (!sig || !sig.trim()) return null;\n  return sig\n    .replace(/^```\\w*\\s*/, '')\n    .replace(/\\s*```$/, '')\n    .replace(/^\\(method\\)\\s*/, '')\n    .replace(/^\\(property\\)\\s*/, '')\n    .replace(/^\\(function\\)\\s*/, '')\n    .replace(/^\\(class\\)\\s*/, '')\n    .replace(/^\\(interface\\)\\s*/, '')\n    .replace(/^\\(enum\\)\\s*/, '')\n    .replace(/^\\(type alias\\)\\s*/, '')\n    .replace(/^\\(const\\)\\s*/, '')\n    .replace(/^\\(var\\)\\s*/, '')\n    .trim() || null;\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { SymbolResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\nimport { cleanSignature } from './clean-signature.js';\n\nexport function symbols(db: ScipDatabase, filePattern: string): SymbolResult[] {\n  const rows = db.all<{\n    start_line: number;\n    end_line: number;\n    sig: string | null;\n    symbol: string;\n    relative_path: string;\n  }>(\n    `SELECT\n      der.start_line,\n      der.end_line,\n      REPLACE(SUBSTR(gs.documentation, INSTR(gs.documentation, '|') + 1), char(10), ' ') AS sig,\n      gs.symbol,\n      d.relative_path\n    FROM defn_enclosing_ranges der\n    JOIN global_symbols gs ON der.symbol_id = gs.id\n    JOIN documents d ON der.document_id = d.id\n    WHERE d.relative_path LIKE ?\n      AND ${db.localSymbolPredicate}\n      ${db.symbolNoise}\n    ORDER BY der.start_line`,\n    `%${filePattern}%`,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({\n      startLine: r.start_line,\n      endLine: r.end_line,\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      signature: cleanSignature(r.sig),\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { MethodResult } from '../types.js';\nimport { leafName } from '../symbol-parser.js';\n\nexport function methods(db: ScipDatabase, className: string): MethodResult[] {\n  const rows = db.all<{\n    start_line: number;\n    end_line: number;\n    symbol: string;\n  }>(\n    `SELECT der.start_line, der.end_line, gs.symbol\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    WHERE gs.symbol LIKE ?\n      AND ${db.localSymbolPredicate}\n      AND gs.symbol LIKE '%().%'\n      ${db.symbolNoise}\n    ORDER BY der.start_line`,\n    `%${className}#%`,\n  );\n\n  return rows.map((r) => ({\n    startLine: r.start_line,\n    endLine: r.end_line,\n    name: leafName(r.symbol),\n  }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { RefResult } from '../types.js';\n\nexport function refs(db: ScipDatabase, symbolPattern: string): RefResult[] {\n  const rows = db.all<{\n    relative_path: string;\n    start_line: number;\n  }>(\n    `SELECT DISTINCT d.relative_path, c.start_line\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d ON c.document_id = d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    WHERE gs.symbol LIKE ?\n      AND ${db.localSymbolPredicate}\n      AND m.role = 0\n    ORDER BY d.relative_path, c.start_line`,\n    `%${symbolPattern}%`,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({\n      relativePath: r.relative_path,\n      line: r.start_line,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { TraceResult } from '../types.js';\nimport { cleanSignature } from './clean-signature.js';\n\nexport function trace(db: ScipDatabase, symbolPattern: string): TraceResult {\n  // Definitions\n  const defRows = db.all<{\n    relative_path: string;\n    start_line: number;\n    end_line: number;\n    sig: string | null;\n  }>(\n    `SELECT d.relative_path, der.start_line, der.end_line,\n      REPLACE(SUBSTR(gs.documentation, INSTR(gs.documentation, '|') + 1), char(10), ' ') AS sig\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE gs.symbol LIKE ?\n      AND ${db.localSymbolPredicate}\n      ${db.symbolNoise}\n    ORDER BY d.relative_path, der.start_line\n    LIMIT 10`,\n    `%${symbolPattern}%`,\n  );\n\n  const definitions = defRows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({\n      relativePath: r.relative_path,\n      startLine: r.start_line,\n      endLine: r.end_line,\n      signature: cleanSignature(r.sig),\n    }));\n\n  // References\n  const refRows = db.all<{ relative_path: string }>(\n    `SELECT DISTINCT d.relative_path\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d ON c.document_id = d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    WHERE gs.symbol LIKE ?\n      AND ${db.localSymbolPredicate}\n      ${db.symbolNoise}\n      AND m.role = 0\n    ORDER BY d.relative_path`,\n    `%${symbolPattern}%`,\n  );\n\n  const referencedBy = refRows\n    .map((r) => r.relative_path)\n    .filter((p) => !db.isIgnored(p));\n\n  return { definitions, referencedBy };\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { DepResult } from '../types.js';\n\n/** What internal files does this file depend on? (forward dependencies) */\nexport function deps(db: ScipDatabase, filePattern: string): DepResult[] {\n  const rows = db.all<{ relative_path: string }>(\n    `SELECT DISTINCT d2.relative_path\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d1 ON c.document_id = d1.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d2 ON der.document_id = d2.id\n    WHERE d1.relative_path LIKE ?\n      AND d2.relative_path <> d1.relative_path\n      AND ${db.localSymbolPredicate}\n    ORDER BY d2.relative_path`,\n    `%${filePattern}%`,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({ relativePath: r.relative_path }));\n}\n\n/** What files depend on this file/module? (reverse dependencies) */\nexport function rdeps(db: ScipDatabase, filePattern: string): DepResult[] {\n  const rows = db.all<{ relative_path: string }>(\n    `SELECT DISTINCT d1.relative_path\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d1 ON c.document_id = d1.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d2 ON der.document_id = d2.id\n    WHERE d2.relative_path LIKE ?\n      AND d1.relative_path NOT LIKE ?\n    ORDER BY d1.relative_path`,\n    `%${filePattern}%`,\n    `%${filePattern}%`,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({ relativePath: r.relative_path }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { SystemResult, SymbolResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\nimport { cleanSignature } from './clean-signature.js';\n\n/** Full system map for a module path: files, symbols, deps in/out */\nexport function system(db: ScipDatabase, modulePattern: string): SystemResult {\n  // Files in this module\n  const fileRows = db.all<{ relative_path: string }>(\n    `SELECT relative_path FROM documents\n     WHERE relative_path LIKE ?\n     ORDER BY relative_path`,\n    `%${modulePattern}%`,\n  );\n  const files = fileRows\n    .map((r) => r.relative_path)\n    .filter((p) => !db.isIgnored(p));\n\n  // Exported symbols\n  const symbolRows = db.all<{\n    start_line: number;\n    end_line: number;\n    symbol: string;\n    sig: string | null;\n  }>(\n    `SELECT der.start_line, der.end_line, gs.symbol,\n      REPLACE(SUBSTR(gs.documentation, INSTR(gs.documentation, '|') + 1), char(10), ' ') AS sig\n    FROM defn_enclosing_ranges der\n    JOIN global_symbols gs ON der.symbol_id = gs.id\n    JOIN documents d ON der.document_id = d.id\n    WHERE d.relative_path LIKE ?\n      AND ${db.localSymbolPredicate}\n      ${db.symbolNoise}\n      AND gs.documentation IS NOT NULL\n    ORDER BY d.relative_path, der.start_line`,\n    `%${modulePattern}%`,\n  );\n  const symbols: SymbolResult[] = symbolRows.map((r) => ({\n    startLine: r.start_line,\n    endLine: r.end_line,\n    symbol: r.symbol,\n    shortName: shortenSymbol(r.symbol),\n    signature: cleanSignature(r.sig),\n  }));\n\n  // Internal dependencies (what this module depends on)\n  const depRows = db.all<{ relative_path: string }>(\n    `SELECT DISTINCT d2.relative_path\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d1 ON c.document_id = d1.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d2 ON der.document_id = d2.id\n    WHERE d1.relative_path LIKE ?\n      AND d2.relative_path NOT LIKE ?\n      AND ${db.localSymbolPredicate}\n    ORDER BY d2.relative_path`,\n    `%${modulePattern}%`,\n    `%${modulePattern}%`,\n  );\n  const dependsOn = depRows\n    .map((r) => r.relative_path)\n    .filter((p) => !db.isIgnored(p));\n\n  // Reverse dependencies (who depends on this module)\n  const rdepRows = db.all<{ relative_path: string }>(\n    `SELECT DISTINCT d1.relative_path\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d1 ON c.document_id = d1.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d2 ON der.document_id = d2.id\n    WHERE d2.relative_path LIKE ?\n      AND d1.relative_path NOT LIKE ?\n    ORDER BY d1.relative_path`,\n    `%${modulePattern}%`,\n    `%${modulePattern}%`,\n  );\n  const dependedOnBy = rdepRows\n    .map((r) => r.relative_path)\n    .filter((p) => !db.isIgnored(p));\n\n  return { files, symbols, dependsOn, dependedOnBy };\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { SurfaceResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/** Public API surface: what symbols do external consumers actually use from this module? */\nexport function surface(db: ScipDatabase, modulePattern: string): SurfaceResult[] {\n  const rows = db.all<{\n    relative_path: string;\n    symbol: string;\n  }>(\n    `SELECT DISTINCT d1.relative_path, gs.symbol\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d1 ON c.document_id = d1.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d2 ON der.document_id = d2.id\n    WHERE d2.relative_path LIKE ?\n      AND d1.relative_path NOT LIKE ?\n      AND ${db.localSymbolPredicate}\n      AND m.role = 0\n    ORDER BY d1.relative_path`,\n    `%${modulePattern}%`,\n    `%${modulePattern}%`,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({\n      consumer: r.relative_path,\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n    }));\n}\n","import type { ScipDatabase } from './db.js';\n\nexport interface SymbolLocation {\n  documentId: number;\n  startLine: number;\n  endLine: number;\n  symbolId: number;\n}\n\nexport interface SymbolMatch extends SymbolLocation {\n  symbol: string;\n  relativePath: string;\n}\n\nexport interface CalleeRow {\n  symbol: string;\n  file: string;\n  chunkId: number;\n}\n\nexport const TEST_FILE_PATTERNS = [\n  '%/__tests__/%',\n  '%.test.%',\n  '%.spec.%',\n  '%/test/%',\n  '%/tests/%',\n  '%_test.%',\n  '%_spec.%',\n  '%/test_%.%',\n  '%/spec_%.%',\n] as const;\n\nexport const TEST_SUPPORT_PATH_PATTERNS = [\n  '%/test-utils/%',\n] as const;\n\nexport function testFileMatchSql(\n  alias: string,\n  patterns: readonly string[] = TEST_FILE_PATTERNS,\n): string {\n  return `(${patterns.map((pattern) => `${alias}.relative_path LIKE '${pattern}'`).join(' OR ')})`;\n}\n\nexport function testFileExclusionSql(\n  alias: string,\n  extraPatterns: readonly string[] = [],\n): string {\n  const patterns = uniquePatterns([...TEST_FILE_PATTERNS, ...extraPatterns]);\n  return patterns\n    .map((pattern) => `${alias}.relative_path NOT LIKE '${pattern}'`)\n    .join('\\n      AND ');\n}\n\nexport function buildFileDepGraph(\n  db: ScipDatabase,\n  scope?: string,\n): Map<string, Set<string>> {\n  const scopeFilter = scope ? `AND d1.relative_path LIKE '%${scope}%'` : '';\n\n  const edges = db.all<{ from_file: string; to_file: string }>(\n    `SELECT DISTINCT\n      d1.relative_path AS from_file,\n      d2.relative_path AS to_file\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d1 ON c.document_id = d1.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d2 ON der.document_id = d2.id\n    WHERE d1.id != d2.id\n      AND m.role = 0\n      ${db.pathExclusionsFor('d1', 'd2')}\n      ${scopeFilter}`,\n  );\n\n  const graph = new Map<string, Set<string>>();\n  for (const edge of edges) {\n    if (db.isIgnored(edge.from_file) || db.isIgnored(edge.to_file)) continue;\n    if (!graph.has(edge.from_file)) graph.set(edge.from_file, new Set());\n    graph.get(edge.from_file)!.add(edge.to_file);\n  }\n\n  return graph;\n}\n\nexport function findFirstSymbolMatch(\n  db: ScipDatabase,\n  symbolPattern: string,\n): SymbolMatch | null {\n  // Handle file:line-line syntax (e.g., \"src/foo.ts:10-50\")\n  const fileLineMatch = symbolPattern.match(/^(.+):(\\d+)-(\\d+)$/);\n  if (fileLineMatch) {\n    const [, filePath, startStr, endStr] = fileLineMatch;\n    const row = db.get<{\n      id: number;\n      symbol: string;\n      document_id: number;\n      start_line: number;\n      end_line: number;\n      relative_path: string;\n    }>(\n      `SELECT gs.id, gs.symbol, der.document_id, der.start_line, der.end_line, d.relative_path\n      FROM global_symbols gs\n      JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n      JOIN documents d ON der.document_id = d.id\n      WHERE d.relative_path LIKE ?\n        AND der.start_line <= ? AND der.end_line >= ?\n        ${db.pathExclusionsFor('d')}\n      ORDER BY (der.end_line - der.start_line) ASC\n      LIMIT 1`,\n      `%${filePath}%`, parseInt(startStr!, 10), parseInt(endStr!, 10),\n    );\n    if (row && !db.isIgnored(row.relative_path)) {\n      return {\n        symbolId: row.id,\n        symbol: row.symbol,\n        documentId: row.document_id,\n        startLine: row.start_line,\n        endLine: row.end_line,\n        relativePath: row.relative_path,\n      };\n    }\n  }\n\n  // Strip parentheses from the pattern to avoid shell escaping issues.\n  // Agents often pass \"functionName()\" — strip the () for matching.\n  const cleaned = symbolPattern.replace(/\\(\\)$/, '').replace(/\\(.*$/, '');\n\n  // Try exact-ish match first (with noise filter), then fallback without noise filter.\n  // The noise filter excludes %().(%  which can incorrectly match some symbols.\n  for (const useNoiseFilter of [true, false]) {\n    const noiseClause = useNoiseFilter ? db.symbolNoiseFor('gs') : '';\n    const row = db.get<{\n      id: number;\n      symbol: string;\n      document_id: number;\n      start_line: number;\n      end_line: number;\n      relative_path: string;\n    }>(\n      `SELECT gs.id, gs.symbol, der.document_id, der.start_line, der.end_line, d.relative_path\n      FROM global_symbols gs\n      JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n      JOIN documents d ON der.document_id = d.id\n      WHERE gs.symbol LIKE ?\n        ${db.pathExclusionsFor('d')}\n        ${noiseClause}\n      ORDER BY (der.end_line - der.start_line) DESC\n      LIMIT 1`,\n      `%${cleaned}%`,\n    );\n\n    if (row && !db.isIgnored(row.relative_path)) {\n      return {\n        symbolId: row.id,\n        symbol: row.symbol,\n        documentId: row.document_id,\n        startLine: row.start_line,\n        endLine: row.end_line,\n        relativePath: row.relative_path,\n      };\n    }\n  }\n\n  return null;\n}\n\nexport function getCalleeRowsForSymbol(\n  db: ScipDatabase,\n  symbol: SymbolLocation,\n  opts: { limit?: number } = {},\n): CalleeRow[] {\n  const rows = db.all<{\n    symbol: string;\n    file: string;\n    chunk_id: number;\n  }>(\n    `SELECT DISTINCT\n      callee_gs.symbol AS symbol,\n      callee_d.relative_path AS file,\n      c.id AS chunk_id\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN global_symbols callee_gs ON m.symbol_id = callee_gs.id\n    JOIN defn_enclosing_ranges callee_der ON callee_gs.id = callee_der.symbol_id\n    JOIN documents callee_d ON callee_der.document_id = callee_d.id\n    WHERE c.document_id = ?\n      AND c.start_line >= ?\n      AND c.end_line <= ?\n      AND m.role = 0\n      AND callee_gs.id != ?\n      ${db.symbolNoiseFor('callee_gs')}\n      ${db.pathExclusionsFor('callee_d')}\n    ORDER BY callee_d.relative_path\n    ${opts.limit ? 'LIMIT ?' : ''}`,\n    ...calleeQueryParams(symbol, opts.limit),\n  );\n\n  return rows.filter((row) => !db.isIgnored(row.file)).map((row) => ({\n    symbol: row.symbol,\n    file: row.file,\n    chunkId: row.chunk_id,\n  }));\n}\n\nfunction calleeQueryParams(\n  symbol: SymbolLocation,\n  limit?: number,\n): number[] {\n  const params = [\n    symbol.documentId,\n    symbol.startLine,\n    symbol.endLine,\n    symbol.symbolId,\n  ];\n\n  if (typeof limit === 'number') {\n    params.push(limit);\n  }\n\n  return params;\n}\n\nfunction uniquePatterns(patterns: readonly string[]): string[] {\n  return [...new Set(patterns)];\n}\n","import type { ScipDatabase } from '../db.js';\nimport { TEST_SUPPORT_PATH_PATTERNS, testFileExclusionSql } from '../query-support.js';\nimport type { DeadOptions, DeadSymbolResult, DeadSummary } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find dead exports: symbols defined locally with no cross-file references.\n * Language-agnostic — works with any SCIP index.\n */\nexport function dead(db: ScipDatabase, opts: DeadOptions = {}): DeadSummary {\n  const {\n    scope,\n    minLoc = 1,\n    includeTests = false,\n    skipBarrels = false,\n    includeMembers = false,\n  } = opts;\n\n  const params: unknown[] = [minLoc];\n  let testFileExclusions = '';\n  let memberExclusion = '';\n\n  if (scope) {\n    params.push(`%${scope}%`);\n  }\n\n  if (!includeTests) {\n    testFileExclusions = `\n      AND ${testFileExclusionSql('d', TEST_SUPPORT_PATH_PATTERNS)}\n    `;\n  }\n\n  if (!includeMembers) {\n    memberExclusion = `AND gs.symbol NOT LIKE '%#%'`;\n  }\n\n  // Barrel file exclusion for the NOT EXISTS subquery\n  const barrelExclusions = skipBarrels\n    ? `AND ref_d.relative_path NOT LIKE '%/index.ts'\n       AND ref_d.relative_path NOT LIKE '%/index.js'\n       AND ref_d.relative_path NOT LIKE '%/mod.rs'\n       AND ref_d.relative_path NOT LIKE '%/__init__.py'`\n    : '';\n\n  const sql = `\n    SELECT\n      d.relative_path,\n      der.start_line,\n      der.end_line,\n      (der.end_line - der.start_line + 1) AS loc,\n      gs.symbol,\n      (SELECT COUNT(*) FROM mentions m2\n       JOIN chunks c2 ON m2.chunk_id = c2.id\n       WHERE m2.symbol_id = gs.id AND m2.role = 0 AND c2.document_id = d.id\n      ) AS same_file_refs\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND (der.end_line - der.start_line + 1) >= ?\n      ${scope ? 'AND d.relative_path LIKE ?' : ''}\n      ${testFileExclusions}\n      ${memberExclusion}\n      AND NOT EXISTS (\n        SELECT 1\n        FROM mentions ref_m\n        JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n        JOIN documents ref_d ON ref_c.document_id = ref_d.id\n        WHERE ref_m.symbol_id = gs.id\n          AND ref_m.role = 0\n          AND ref_d.id != d.id\n          ${barrelExclusions}\n      )\n    ORDER BY (der.end_line - der.start_line + 1) DESC, d.relative_path, der.start_line\n  `;\n\n  const rows = db.all<{\n    relative_path: string;\n    start_line: number;\n    end_line: number;\n    loc: number;\n    symbol: string;\n    same_file_refs: number;\n  }>(sql, ...params);\n\n  let deadCodeCount = 0;\n  let fileInternalCount = 0;\n  let totalLoc = 0;\n\n  const symbols: DeadSymbolResult[] = rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => {\n      // dead-code: zero references anywhere (not even in same file) — safe to delete\n      // file-internal: referenced within same file but never cross-file —\n      //   may be a private helper (fine) or a forgotten export (needs review)\n      const kind = r.same_file_refs === 0 ? 'dead-code' : 'file-internal';\n      if (kind === 'dead-code') deadCodeCount++;\n      else fileInternalCount++;\n      totalLoc += r.loc;\n\n      return {\n        relativePath: r.relative_path,\n        startLine: r.start_line,\n        endLine: r.end_line,\n        loc: r.loc,\n        symbol: r.symbol,\n        shortName: shortenSymbol(r.symbol),\n        sameFileRefs: r.same_file_refs,\n        kind,\n      };\n    });\n\n  return {\n    symbols,\n    totalCount: symbols.length,\n    deadCodeCount,\n    fileInternalCount,\n    totalLoc,\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { HotspotResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find the most-referenced symbols in the codebase — the choke points\n * where changes have the widest blast radius.\n */\nexport function hotspots(\n  db: ScipDatabase,\n  opts: { limit?: number; scope?: string } = {},\n): HotspotResult[] {\n  const { limit = 30, scope } = opts;\n\n  const scopeFilter = scope ? `AND def_d.relative_path LIKE '%${scope}%'` : '';\n\n  const rows = db.all<{\n    symbol: string;\n    ref_count: number;\n    file_count: number;\n    defined_in: string;\n  }>(\n    `SELECT\n      gs.symbol,\n      COUNT(*) AS ref_count,\n      COUNT(DISTINCT ref_d.id) AS file_count,\n      def_d.relative_path AS defined_in\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents ref_d ON c.document_id = ref_d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents def_d ON der.document_id = def_d.id\n    WHERE m.role = 0\n      ${db.pathExclusionsFor('def_d')}\n      ${db.symbolNoiseFor('gs')}\n      ${scopeFilter}\n    GROUP BY gs.id\n    ORDER BY ref_count DESC\n    LIMIT ?`,\n    limit,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.defined_in))\n    .map((r) => ({\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      refCount: r.ref_count,\n      fileCount: r.file_count,\n      definedIn: r.defined_in,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { ImportResult, UnusedImportResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * What symbols does this file import?\n * Uses role=2 (import) from the SCIP mentions table.\n */\nexport function imports(db: ScipDatabase, filePattern: string): ImportResult[] {\n  const rows = db.all<{\n    symbol: string;\n    from_file: string;\n  }>(\n    `SELECT DISTINCT gs.symbol, def_d.relative_path AS from_file\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents imp_d ON c.document_id = imp_d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    LEFT JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    LEFT JOIN documents def_d ON der.document_id = def_d.id\n    WHERE imp_d.relative_path LIKE ?\n      AND m.role = 2\n    ORDER BY def_d.relative_path, gs.symbol`,\n    `%${filePattern}%`,\n  );\n\n  return rows.map((r) => ({\n    symbol: r.symbol,\n    shortName: shortenSymbol(r.symbol),\n    fromFile: r.from_file ?? '(external)',\n  }));\n}\n\n/**\n * Which files import this symbol?\n */\nexport function importedBy(db: ScipDatabase, symbolPattern: string): ImportResult[] {\n  const rows = db.all<{\n    symbol: string;\n    importer: string;\n  }>(\n    `SELECT DISTINCT gs.symbol, d.relative_path AS importer\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d ON c.document_id = d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    WHERE gs.symbol LIKE ?\n      AND m.role = 2\n    ORDER BY d.relative_path`,\n    `%${symbolPattern}%`,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.importer))\n    .map((r) => ({\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      fromFile: r.importer,\n    }));\n}\n\n/**\n * Find imports in a file that are never referenced (role=0) in the same file.\n * These are likely unused imports.\n */\nexport function unusedImports(db: ScipDatabase, filePattern: string): UnusedImportResult[] {\n  const rows = db.all<{\n    symbol: string;\n    imported_in: string;\n  }>(\n    `SELECT gs.symbol, d.relative_path AS imported_in\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d ON c.document_id = d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    WHERE d.relative_path LIKE ?\n      AND m.role = 2\n      AND NOT EXISTS (\n        SELECT 1\n        FROM mentions ref_m\n        JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n        WHERE ref_m.symbol_id = gs.id\n          AND ref_m.role = 0\n          AND ref_c.document_id = d.id\n      )\n    ORDER BY d.relative_path, gs.symbol`,\n    `%${filePattern}%`,\n  );\n\n  return rows.map((r) => ({\n    symbol: r.symbol,\n    shortName: shortenSymbol(r.symbol),\n    importedIn: r.imported_in,\n  }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { OutlineNode } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Build a tree-structured outline of symbols in a file,\n * using the enclosing_symbol field to establish parent-child relationships.\n */\nexport function outline(db: ScipDatabase, filePattern: string): OutlineNode[] {\n  const rows = db.all<{\n    symbol: string;\n    enclosing_symbol: string | null;\n    start_line: number;\n    end_line: number;\n  }>(\n    `SELECT gs.symbol, gs.enclosing_symbol, der.start_line, der.end_line\n    FROM defn_enclosing_ranges der\n    JOIN global_symbols gs ON der.symbol_id = gs.id\n    JOIN documents d ON der.document_id = d.id\n    WHERE d.relative_path LIKE ?\n      ${db.symbolNoise}\n    ORDER BY der.start_line`,\n    `%${filePattern}%`,\n  );\n\n  // Build a map of symbol -> node\n  const nodeMap = new Map<string, OutlineNode>();\n  const roots: OutlineNode[] = [];\n\n  for (const r of rows) {\n    const node: OutlineNode = {\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      startLine: r.start_line,\n      endLine: r.end_line,\n      children: [],\n    };\n    nodeMap.set(r.symbol, node);\n  }\n\n  // Wire up parent-child via enclosing_symbol\n  for (const r of rows) {\n    const node = nodeMap.get(r.symbol)!;\n    if (r.enclosing_symbol && nodeMap.has(r.enclosing_symbol)) {\n      nodeMap.get(r.enclosing_symbol)!.children.push(node);\n    } else {\n      roots.push(node);\n    }\n  }\n\n  return roots;\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { MemberResult } from '../types.js';\nimport { shortenSymbol, parseSymbol } from '../symbol-parser.js';\nimport type { ScipSymbol } from '../types.js';\n\n/**\n * Find all direct children of a symbol (methods, fields, nested types).\n * Uses the enclosing_symbol relationship in global_symbols.\n */\nexport function members(db: ScipDatabase, symbolPattern: string): MemberResult[] {\n  // First find the parent symbol(s)\n  const parents = db.all<{ symbol: string }>(\n    `SELECT symbol FROM global_symbols WHERE symbol LIKE ?`,\n    `%${symbolPattern}%`,\n  );\n\n  if (parents.length === 0) return [];\n\n  // Find children whose enclosing_symbol matches any parent\n  const placeholders = parents.map(() => '?').join(',');\n  const parentSymbols = parents.map((p) => p.symbol);\n\n  const rows = db.all<{\n    symbol: string;\n    start_line: number;\n    end_line: number;\n  }>(\n    `SELECT gs.symbol, der.start_line, der.end_line\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    WHERE gs.enclosing_symbol IN (${placeholders})\n      ${db.symbolNoise}\n    ORDER BY der.start_line`,\n    ...parentSymbols,\n  );\n\n  return rows.map((r) => {\n    const parsed = parseSymbol(r.symbol);\n    let kind = 'unknown';\n    if (!('kind' in parsed)) {\n      const sym = parsed as ScipSymbol;\n      const last = sym.descriptors[sym.descriptors.length - 1];\n      if (last) kind = last.suffix;\n    }\n\n    return {\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      startLine: r.start_line,\n      endLine: r.end_line,\n      kind,\n    };\n  });\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { FanResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Fan-in: how many distinct files reference this symbol.\n * High fan-in = widely depended upon = high blast radius for changes.\n */\nexport function fanIn(\n  db: ScipDatabase,\n  symbolPattern: string,\n): FanResult[] {\n  const rows = db.all<{\n    symbol: string;\n    file_count: number;\n  }>(\n    `SELECT gs.symbol, COUNT(DISTINCT c.document_id) AS file_count\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    WHERE gs.symbol LIKE ?\n      AND m.role = 0\n    GROUP BY gs.id\n    ORDER BY file_count DESC`,\n    `%${symbolPattern}%`,\n  );\n\n  return rows.map((r) => ({\n    name: shortenSymbol(r.symbol),\n    count: r.file_count,\n  }));\n}\n\n/**\n * Fan-out: how many external symbols does this file reference.\n * High fan-out = depends on many things = fragile to upstream changes.\n */\nexport function fanOut(\n  db: ScipDatabase,\n  filePattern: string,\n): FanResult[] {\n  const rows = db.all<{\n    relative_path: string;\n    symbol_count: number;\n  }>(\n    `SELECT d.relative_path, COUNT(DISTINCT gs.id) AS symbol_count\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d ON c.document_id = d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents def_d ON der.document_id = def_d.id\n    WHERE d.relative_path LIKE ?\n      AND m.role = 0\n      AND def_d.id != d.id\n    GROUP BY d.id\n    ORDER BY symbol_count DESC`,\n    `%${filePattern}%`,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({\n      name: r.relative_path,\n      count: r.symbol_count,\n    }));\n}\n\n/**\n * Top fan-in across the whole codebase — the most depended-on symbols.\n */\nexport function topFanIn(\n  db: ScipDatabase,\n  opts: { limit?: number; scope?: string } = {},\n): FanResult[] {\n  const { limit = 30, scope } = opts;\n  const scopeFilter = scope\n    ? `AND def_d.relative_path LIKE '%${scope}%'`\n    : '';\n\n  const rows = db.all<{\n    symbol: string;\n    file_count: number;\n  }>(\n    `SELECT gs.symbol, COUNT(DISTINCT c.document_id) AS file_count\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents def_d ON der.document_id = def_d.id\n    WHERE m.role = 0\n      ${db.pathExclusionsFor('def_d')}\n      ${db.symbolNoiseFor('gs')}\n      ${scopeFilter}\n    GROUP BY gs.id\n    HAVING file_count > 1\n    ORDER BY file_count DESC\n    LIMIT ?`,\n    limit,\n  );\n\n  return rows.map((r) => ({\n    name: shortenSymbol(r.symbol),\n    count: r.file_count,\n  }));\n}\n\n/**\n * Top fan-out across the whole codebase — files that depend on the most external symbols.\n */\nexport function topFanOut(\n  db: ScipDatabase,\n  opts: { limit?: number; scope?: string } = {},\n): FanResult[] {\n  const { limit = 30, scope } = opts;\n  const scopeFilter = scope\n    ? `AND d.relative_path LIKE '%${scope}%'`\n    : '';\n\n  const rows = db.all<{\n    relative_path: string;\n    symbol_count: number;\n  }>(\n    `SELECT d.relative_path, COUNT(DISTINCT gs.id) AS symbol_count\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d ON c.document_id = d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents def_d ON der.document_id = def_d.id\n    WHERE m.role = 0\n      AND def_d.id != d.id\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n      ${scopeFilter}\n    GROUP BY d.id\n    ORDER BY symbol_count DESC\n    LIMIT ?`,\n    limit,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({\n      name: r.relative_path,\n      count: r.symbol_count,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { CouplingResult } from '../types.js';\n\n/**\n * Measure coupling between two files: how many symbols do they share\n * (symbols defined in one and referenced in the other, or vice versa).\n */\nexport function coupling(\n  db: ScipDatabase,\n  file1: string,\n  file2: string,\n): CouplingResult {\n  const row = db.get<{ shared: number }>(\n    `SELECT COUNT(DISTINCT gs.id) AS shared\n    FROM global_symbols gs\n    WHERE (\n      -- Defined in file1, referenced in file2\n      EXISTS (\n        SELECT 1 FROM defn_enclosing_ranges der\n        JOIN documents d ON der.document_id = d.id\n        WHERE der.symbol_id = gs.id AND d.relative_path LIKE ?\n      )\n      AND EXISTS (\n        SELECT 1 FROM mentions m\n        JOIN chunks c ON m.chunk_id = c.id\n        JOIN documents d ON c.document_id = d.id\n        WHERE m.symbol_id = gs.id AND m.role = 0 AND d.relative_path LIKE ?\n      )\n    ) OR (\n      -- Defined in file2, referenced in file1\n      EXISTS (\n        SELECT 1 FROM defn_enclosing_ranges der\n        JOIN documents d ON der.document_id = d.id\n        WHERE der.symbol_id = gs.id AND d.relative_path LIKE ?\n      )\n      AND EXISTS (\n        SELECT 1 FROM mentions m\n        JOIN chunks c ON m.chunk_id = c.id\n        JOIN documents d ON c.document_id = d.id\n        WHERE m.symbol_id = gs.id AND m.role = 0 AND d.relative_path LIKE ?\n      )\n    )`,\n    `%${file1}%`, `%${file2}%`,\n    `%${file2}%`, `%${file1}%`,\n  );\n\n  return {\n    file1,\n    file2,\n    sharedSymbols: row?.shared ?? 0,\n  };\n}\n\n/**\n * Find the most coupled file pairs in the codebase.\n */\nexport function topCoupling(\n  db: ScipDatabase,\n  opts: { limit?: number; scope?: string } = {},\n): CouplingResult[] {\n  const { limit = 20, scope } = opts;\n  const scopeFilter = scope\n    ? `AND d1.relative_path LIKE '%${scope}%' AND d2.relative_path LIKE '%${scope}%'`\n    : '';\n\n  // Find file pairs that share the most symbols (one defines, other references)\n  const rows = db.all<{\n    file1: string;\n    file2: string;\n    shared: number;\n  }>(\n    `SELECT\n      def_d.relative_path AS file1,\n      ref_d.relative_path AS file2,\n      COUNT(DISTINCT gs.id) AS shared\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents ref_d ON c.document_id = ref_d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents def_d ON der.document_id = def_d.id\n    WHERE m.role = 0\n      AND def_d.id != ref_d.id\n      ${db.pathExclusionsFor('def_d', 'ref_d')}\n      ${scopeFilter}\n    GROUP BY def_d.id, ref_d.id\n    ORDER BY shared DESC\n    LIMIT ?`,\n    limit,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.file1) && !db.isIgnored(r.file2))\n    .map((r) => ({\n      file1: r.file1,\n      file2: r.file2,\n      sharedSymbols: r.shared,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport { buildFileDepGraph } from '../query-support.js';\nimport type { CycleResult } from '../types.js';\n\n/**\n * Detect circular dependency chains between files.\n * A cycle exists when file A depends on B, B depends on C, and C depends on A.\n *\n * Uses the same dependency edges as the `deps` command (symbol definitions\n * referenced across files), then runs DFS cycle detection.\n */\nexport function cycles(\n  db: ScipDatabase,\n  opts: { scope?: string; maxDepth?: number } = {},\n): CycleResult[] {\n  const { scope, maxDepth = 10 } = opts;\n  const graph = buildFileDepGraph(db, scope);\n\n  // DFS cycle detection\n  const allCycles: CycleResult[] = [];\n  const visited = new Set<string>();\n  const inStack = new Set<string>();\n  const stack: string[] = [];\n\n  function dfs(node: string, depth: number): void {\n    if (depth > maxDepth) return;\n    if (inStack.has(node)) {\n      // Found a cycle — extract it from the stack\n      const cycleStart = stack.indexOf(node);\n      if (cycleStart !== -1) {\n        const cyclePath = stack.slice(cycleStart).concat(node);\n        // Normalize: start from the lexicographically smallest file\n        const minIdx = cyclePath.indexOf(\n          cyclePath.reduce((a, b) => (a < b ? a : b)),\n        );\n        const normalized = [\n          ...cyclePath.slice(minIdx, -1),\n          ...cyclePath.slice(0, minIdx),\n          cyclePath[minIdx]!,\n        ];\n        // Deduplicate\n        const key = normalized.join(' -> ');\n        if (!seenCycles.has(key)) {\n          seenCycles.add(key);\n          allCycles.push({ path: normalized });\n        }\n      }\n      return;\n    }\n    if (visited.has(node)) return;\n\n    visited.add(node);\n    inStack.add(node);\n    stack.push(node);\n\n    const neighbors = graph.get(node);\n    if (neighbors) {\n      for (const neighbor of neighbors) {\n        dfs(neighbor, depth + 1);\n      }\n    }\n\n    stack.pop();\n    inStack.delete(node);\n  }\n\n  const seenCycles = new Set<string>();\n  for (const node of graph.keys()) {\n    if (!visited.has(node)) {\n      dfs(node, 0);\n    }\n  }\n\n  // Sort by cycle length (shorter cycles are more actionable)\n  allCycles.sort((a, b) => a.path.length - b.path.length);\n\n  return allCycles;\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { BottleneckResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find coupling hubs: symbols with both high fan-in (many consumers)\n * AND high fan-out (references many other symbols).\n *\n * These are the most dangerous symbols to change — they sit at the\n * intersection of many dependency paths. Score = fanIn * fanOut.\n */\nexport function bottlenecks(\n  db: ScipDatabase,\n  opts: { limit?: number; scope?: string; minFanIn?: number; minFanOut?: number } = {},\n): BottleneckResult[] {\n  const { limit = 20, scope, minFanIn = 2, minFanOut = 2 } = opts;\n  const scopeFilter = scope ? `AND def_d.relative_path LIKE '%${scope}%'` : '';\n\n  // Use a wrapping query to filter on computed columns\n  const rows = db.all<{\n    symbol: string;\n    defined_in: string;\n    fan_in: number;\n    fan_out: number;\n  }>(\n    `SELECT * FROM (\n      SELECT\n        gs.symbol,\n        def_d.relative_path AS defined_in,\n        (SELECT COUNT(DISTINCT ref_c.document_id)\n         FROM mentions ref_m\n         JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n         WHERE ref_m.symbol_id = gs.id AND ref_m.role = 0\n        ) AS fan_in,\n        (SELECT COUNT(DISTINCT ref_gs.id)\n         FROM mentions ref_m\n         JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n         JOIN global_symbols ref_gs ON ref_m.symbol_id = ref_gs.id\n         JOIN defn_enclosing_ranges ref_der ON ref_gs.id = ref_der.symbol_id\n         WHERE ref_c.document_id = def_d.id\n           AND ref_m.role = 0\n           AND ref_der.document_id != def_d.id\n        ) AS fan_out\n      FROM global_symbols gs\n      JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n      JOIN documents def_d ON der.document_id = def_d.id\n      WHERE 1 = 1\n        ${db.pathExclusionsFor('def_d')}\n        ${db.symbolNoiseFor('gs')}\n        ${scopeFilter}\n    ) WHERE fan_in >= ? AND fan_out >= ?\n    ORDER BY (fan_in * fan_out) DESC\n    LIMIT ?`,\n    minFanIn, minFanOut, limit,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.defined_in))\n    .map((r) => ({\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      fanIn: r.fan_in,\n      fanOut: r.fan_out,\n      score: r.fan_in * r.fan_out,\n      definedIn: r.defined_in,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport { testFileExclusionSql } from '../query-support.js';\nimport type { IsolatedResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find isolated symbols: defined locally, referenced by nothing,\n * and referencing nothing external. These are truly orphaned code —\n * not just unused exports, but completely disconnected from the graph.\n */\nexport function isolated(\n  db: ScipDatabase,\n  opts: { scope?: string; minLoc?: number } = {},\n): IsolatedResult[] {\n  const { scope, minLoc = 3 } = opts;\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  const rows = db.all<{\n    symbol: string;\n    relative_path: string;\n    start_line: number;\n    end_line: number;\n    loc: number;\n  }>(\n    `SELECT\n      gs.symbol,\n      d.relative_path,\n      der.start_line,\n      der.end_line,\n      (der.end_line - der.start_line + 1) AS loc\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      AND ${testFileExclusionSql('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND gs.symbol NOT LIKE '%#%'\n      AND (der.end_line - der.start_line + 1) >= ?\n      ${scopeFilter}\n      -- No cross-file references TO this symbol\n      AND NOT EXISTS (\n        SELECT 1 FROM mentions m\n        JOIN chunks c ON m.chunk_id = c.id\n        WHERE m.symbol_id = gs.id AND m.role = 0 AND c.document_id != d.id\n      )\n      -- No same-file references either\n      AND NOT EXISTS (\n        SELECT 1 FROM mentions m\n        JOIN chunks c ON m.chunk_id = c.id\n        WHERE m.symbol_id = gs.id AND m.role = 0 AND c.document_id = d.id\n      )\n    ORDER BY loc DESC, d.relative_path`,\n    minLoc,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      relativePath: r.relative_path,\n      startLine: r.start_line,\n      endLine: r.end_line,\n      loc: r.loc,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { ByKindResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * SCIP SymbolInformation.Kind enum values.\n * From: https://github.com/sourcegraph/scip/blob/main/scip.proto\n */\nconst KIND_NAMES: Record<number, string> = {\n  0: 'UnspecifiedKind',\n  1: 'AbstractMethod',\n  2: 'Accessor',\n  3: 'Array',\n  4: 'Assertion',\n  5: 'AssociatedType',\n  6: 'Attribute',\n  7: 'Axiom',\n  8: 'Boolean',\n  9: 'Class',\n  10: 'Constant',\n  11: 'Constructor',\n  12: 'Contract',\n  13: 'DataFamily',\n  14: 'DefinitionMacro',\n  15: 'Delegate',\n  16: 'Enum',\n  17: 'EnumMember',\n  18: 'Error',\n  19: 'Event',\n  20: 'Fact',\n  21: 'Field',\n  22: 'File',\n  23: 'Function',\n  24: 'Getter',\n  25: 'Grammar',\n  26: 'Instance',\n  27: 'Interface',\n  28: 'Key',\n  29: 'Lang',\n  30: 'Lemma',\n  31: 'Library',\n  32: 'Macro',\n  33: 'Method',\n  34: 'MethodAlias',\n  35: 'MethodReceiver',\n  36: 'MethodSpecification',\n  37: 'Message',\n  38: 'Modifier',\n  39: 'Module',\n  40: 'Namespace',\n  41: 'Null',\n  42: 'Number',\n  43: 'Object',\n  44: 'Operator',\n  45: 'Package',\n  46: 'PackageObject',\n  47: 'Parameter',\n  48: 'ParameterLabel',\n  49: 'Pattern',\n  50: 'Predicate',\n  51: 'Property',\n  52: 'Protocol',\n  53: 'ProtocolMethod',\n  54: 'PureVirtualMethod',\n  55: 'Quasiquoter',\n  56: 'SelfParameter',\n  57: 'Setter',\n  58: 'Signature',\n  59: 'SingletonClass',\n  60: 'SingletonMethod',\n  61: 'StaticDataMember',\n  62: 'StaticEvent',\n  63: 'StaticField',\n  64: 'StaticMethod',\n  65: 'StaticProperty',\n  66: 'StaticVariable',\n  67: 'String',\n  68: 'Struct',\n  69: 'Subscript',\n  70: 'Tactic',\n  71: 'Theorem',\n  72: 'ThisParameter',\n  73: 'Trait',\n  74: 'TraitMethod',\n  75: 'Type',\n  76: 'TypeAlias',\n  77: 'TypeClass',\n  78: 'TypeClassMethod',\n  79: 'TypeFamily',\n  80: 'TypeParameter',\n  81: 'Union',\n  82: 'Value',\n  83: 'Variable',\n};\n\n/** Reverse lookup: name -> kind number */\nconst KIND_BY_NAME = new Map<string, number>();\nfor (const [k, v] of Object.entries(KIND_NAMES)) {\n  KIND_BY_NAME.set(v.toLowerCase(), Number(k));\n}\n\n/**\n * Find symbols by SCIP kind (class, interface, enum, function, etc.)\n */\nexport function byKind(\n  db: ScipDatabase,\n  kindQuery: string,\n  opts: { scope?: string; limit?: number } = {},\n): ByKindResult[] {\n  const { scope, limit = 100 } = opts;\n\n  // Resolve kind: accept number or name\n  let kindNum: number | null = null;\n  const asNum = parseInt(kindQuery, 10);\n  if (!isNaN(asNum)) {\n    kindNum = asNum;\n  } else {\n    kindNum = KIND_BY_NAME.get(kindQuery.toLowerCase()) ?? null;\n    // Fuzzy match: try partial name\n    if (kindNum === null) {\n      for (const [name, num] of KIND_BY_NAME) {\n        if (name.includes(kindQuery.toLowerCase())) {\n          kindNum = num;\n          break;\n        }\n      }\n    }\n  }\n\n  if (kindNum === null) {\n    return [];\n  }\n\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  // Check if the index actually has kind data populated\n  const hasKinds = db.get<{ c: number }>(\n    `SELECT COUNT(*) AS c FROM global_symbols WHERE kind IS NOT NULL`,\n  );\n  if (!hasKinds || hasKinds.c === 0) {\n    return []; // Indexer doesn't populate kind field\n  }\n\n  const rows = db.all<{\n    symbol: string;\n    kind: number;\n    relative_path: string;\n    start_line: number;\n    end_line: number;\n  }>(\n    `SELECT gs.symbol, gs.kind, d.relative_path, der.start_line, der.end_line\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE gs.kind = ?\n      ${db.pathExclusionsFor('d')}\n      ${scopeFilter}\n    ORDER BY d.relative_path, der.start_line\n    LIMIT ?`,\n    kindNum, limit,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.relative_path))\n    .map((r) => ({\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      kind: r.kind,\n      kindName: KIND_NAMES[r.kind] ?? 'Unknown',\n      relativePath: r.relative_path,\n      startLine: r.start_line,\n      endLine: r.end_line,\n    }));\n}\n\n/** List all symbol kinds present in the index with counts */\nexport function kindCounts(\n  db: ScipDatabase,\n  opts: { scope?: string } = {},\n): Array<{ kind: number; kindName: string; count: number }> {\n  const scopeFilter = opts.scope\n    ? `AND d.relative_path LIKE '%${opts.scope}%'`\n    : '';\n\n  const rows = db.all<{ kind: number; cnt: number }>(\n    `SELECT gs.kind, COUNT(*) AS cnt\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      AND gs.kind IS NOT NULL\n      AND gs.kind != 0\n      ${scopeFilter}\n    GROUP BY gs.kind\n    ORDER BY cnt DESC`,\n  );\n\n  return rows.map((r) => ({\n    kind: r.kind,\n    kindName: KIND_NAMES[r.kind] ?? 'Unknown',\n    count: r.cnt,\n  }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport { TEST_FILE_PATTERNS, testFileExclusionSql, testFileMatchSql } from '../query-support.js';\nimport type { TestCoverageResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Check if a symbol is referenced by any test file.\n * Reports which test files cover (reference) each matching symbol.\n */\nexport function testCoverage(\n  db: ScipDatabase,\n  symbolPattern: string,\n): TestCoverageResult[] {\n  // Find matching symbols\n  const syms = db.all<{\n    id: number;\n    symbol: string;\n    relative_path: string;\n  }>(\n    `SELECT gs.id, gs.symbol, d.relative_path\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE gs.symbol LIKE ?\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n    ORDER BY d.relative_path`,\n    `%${symbolPattern}%`,\n  );\n\n  const testPatternSql = testFileMatchSql('ref_d', TEST_FILE_PATTERNS);\n\n  return syms\n    .filter((s) => !db.isIgnored(s.relative_path))\n    .map((s) => {\n      // Find test files that reference this symbol\n      const testFiles = db.all<{ relative_path: string }>(\n        `SELECT DISTINCT ref_d.relative_path\n        FROM mentions m\n        JOIN chunks c ON m.chunk_id = c.id\n        JOIN documents ref_d ON c.document_id = ref_d.id\n        WHERE m.symbol_id = ?\n          AND m.role = 0\n          AND (${testPatternSql})\n        ORDER BY ref_d.relative_path`,\n        s.id,\n      ).map((r) => r.relative_path);\n\n      return {\n        symbol: s.symbol,\n        shortName: shortenSymbol(s.symbol),\n        definedIn: s.relative_path,\n        testFiles,\n        covered: testFiles.length > 0,\n      };\n    });\n}\n\n/**\n * Summary: what percentage of symbols in scope are referenced by test files?\n */\nexport function testCoverageSummary(\n  db: ScipDatabase,\n  opts: { scope?: string; minLoc?: number } = {},\n): { total: number; covered: number; uncovered: number; percent: number } {\n  const { scope, minLoc = 3 } = opts;\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n  const testPatternSql = testFileExclusionSql('d');\n\n  const symbols = db.all<{ id: number }>(\n    `SELECT gs.id\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      AND ${testPatternSql}\n      ${db.symbolNoiseFor('gs')}\n      AND gs.symbol NOT LIKE '%#%'\n      AND (der.end_line - der.start_line + 1) >= ?\n      ${scopeFilter}`,\n    minLoc,\n  );\n\n  const testRefSql = testFileMatchSql('ref_d', TEST_FILE_PATTERNS);\n\n  let covered = 0;\n  for (const s of symbols) {\n    const hasTest = db.get<{ c: number }>(\n      `SELECT COUNT(*) AS c FROM mentions m\n       JOIN chunks c ON m.chunk_id = c.id\n       JOIN documents ref_d ON c.document_id = ref_d.id\n       WHERE m.symbol_id = ? AND m.role = 0 AND (${testRefSql})`,\n      s.id,\n    );\n    if (hasTest && hasTest.c > 0) covered++;\n  }\n\n  const total = symbols.length;\n  return {\n    total,\n    covered,\n    uncovered: total - covered,\n    percent: total > 0 ? Math.round((covered / total) * 100) : 0,\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { DocCoverageResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Check documentation coverage: what percentage of symbols have doc strings?\n * Reports overall stats and lists undocumented symbols.\n */\nexport function docCoverage(\n  db: ScipDatabase,\n  opts: { scope?: string; minLoc?: number; limit?: number } = {},\n): DocCoverageResult {\n  const { scope, minLoc = 3, limit = 50 } = opts;\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  // Count all local symbols meeting the threshold\n  const totalRow = db.get<{ c: number }>(\n    `SELECT COUNT(*) AS c\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND gs.symbol NOT LIKE '%#%'\n      AND (der.end_line - der.start_line + 1) >= ?\n      ${scopeFilter}`,\n    minLoc,\n  );\n\n  const docRow = db.get<{ c: number }>(\n    `SELECT COUNT(*) AS c\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND gs.symbol NOT LIKE '%#%'\n      AND (der.end_line - der.start_line + 1) >= ?\n      AND gs.documentation IS NOT NULL\n      AND gs.documentation != ''\n      ${scopeFilter}`,\n    minLoc,\n  );\n\n  const total = totalRow?.c ?? 0;\n  const documented = docRow?.c ?? 0;\n\n  // Get undocumented symbols\n  const undocRows = db.all<{\n    symbol: string;\n    relative_path: string;\n    start_line: number;\n  }>(\n    `SELECT gs.symbol, d.relative_path, der.start_line\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND gs.symbol NOT LIKE '%#%'\n      AND (der.end_line - der.start_line + 1) >= ?\n      AND (gs.documentation IS NULL OR gs.documentation = '')\n      ${scopeFilter}\n    ORDER BY d.relative_path, der.start_line\n    LIMIT ?`,\n    minLoc, limit,\n  );\n\n  return {\n    totalSymbols: total,\n    documented,\n    undocumented: total - documented,\n    coveragePercent: total > 0 ? Math.round((documented / total) * 100) : 0,\n    undocumentedSymbols: undocRows\n      .filter((r) => !db.isIgnored(r.relative_path))\n      .map((r) => ({\n        symbol: r.symbol,\n        shortName: shortenSymbol(r.symbol),\n        relativePath: r.relative_path,\n        startLine: r.start_line,\n      })),\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport { buildFileDepGraph } from '../query-support.js';\nimport type { DeepChainResult } from '../types.js';\n\n/**\n * Find the longest transitive dependency chains between files.\n * A chain A → B → C → D means A depends on B, B on C, C on D.\n *\n * Long chains = high coupling depth = changes at the end ripple through many layers.\n */\nexport function deepChains(\n  db: ScipDatabase,\n  opts: { limit?: number; scope?: string; minDepth?: number } = {},\n): DeepChainResult[] {\n  const { limit = 10, scope, minDepth = 3 } = opts;\n  const graph = buildFileDepGraph(db, scope);\n\n  // DFS to find longest paths (with cycle detection)\n  const results: DeepChainResult[] = [];\n\n  function dfs(node: string, path: string[], visited: Set<string>): void {\n    const neighbors = graph.get(node);\n    if (!neighbors || neighbors.size === 0) {\n      if (path.length >= minDepth) {\n        results.push({ chain: [...path], depth: path.length });\n      }\n      return;\n    }\n\n    let extended = false;\n    for (const next of neighbors) {\n      if (visited.has(next)) continue; // skip cycles\n      visited.add(next);\n      path.push(next);\n      dfs(next, path, visited);\n      path.pop();\n      visited.delete(next);\n      extended = true;\n    }\n\n    // If no unvisited neighbors, this is a leaf in this path\n    if (!extended && path.length >= minDepth) {\n      results.push({ chain: [...path], depth: path.length });\n    }\n  }\n\n  // Start DFS from each node\n  for (const startNode of graph.keys()) {\n    const visited = new Set<string>([startNode]);\n    dfs(startNode, [startNode], visited);\n\n    // Early termination if we have enough results\n    if (results.length > limit * 10) break;\n  }\n\n  // Sort by depth descending, take top N\n  results.sort((a, b) => b.depth - a.depth);\n  return results.slice(0, limit);\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { HierarchyNode } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Walk the enclosing_symbol chain upward to show a symbol's ancestry.\n * e.g., method → class → module → file\n *\n * Falls back to parsing the SCIP symbol descriptor chain when\n * enclosing_symbol is not populated by the indexer.\n */\nexport function hierarchy(db: ScipDatabase, symbolPattern: string): HierarchyNode[] {\n  // Find the symbol\n  const sym = db.get<{ symbol: string; enclosing_symbol: string | null }>(\n    `SELECT symbol, enclosing_symbol FROM global_symbols\n     WHERE symbol LIKE ? LIMIT 1`,\n    `%${symbolPattern}%`,\n  );\n\n  if (!sym) return [];\n\n  const chain: HierarchyNode[] = [\n    { symbol: sym.symbol, shortName: shortenSymbol(sym.symbol), depth: 0 },\n  ];\n\n  // Walk enclosing_symbol chain if available\n  let current = sym.enclosing_symbol;\n  let depth = 1;\n  const seen = new Set<string>([sym.symbol]);\n\n  while (current && !seen.has(current) && depth < 20) {\n    seen.add(current);\n    const parent = db.get<{ symbol: string; enclosing_symbol: string | null }>(\n      `SELECT symbol, enclosing_symbol FROM global_symbols WHERE symbol = ?`,\n      current,\n    );\n    if (!parent) break;\n\n    chain.push({\n      symbol: parent.symbol,\n      shortName: shortenSymbol(parent.symbol),\n      depth,\n    });\n    current = parent.enclosing_symbol;\n    depth++;\n  }\n\n  return chain;\n}\n","import type { ScipDatabase } from '../db.js';\nimport { findFirstSymbolMatch, getCalleeRowsForSymbol } from '../query-support.js';\nimport type { CallGraphResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Build a call graph for a symbol: who calls it (incoming) and\n * what it calls (outgoing).\n *\n * Incoming: other symbols whose definition ranges contain a reference to this symbol.\n * Outgoing: symbols referenced within this symbol's definition range.\n */\nexport function callGraph(db: ScipDatabase, symbolPattern: string): CallGraphResult | null {\n  // Find the target symbol and its definition range\n  const target = findFirstSymbolMatch(db, symbolPattern);\n\n  if (!target) return null;\n\n  // CALLERS: symbols whose definition ranges contain a reference to our target.\n  // Find chunks that reference our symbol, then find which symbol's definition encloses that chunk.\n  const callerRows = db.all<{\n    caller_symbol: string;\n    caller_file: string;\n  }>(\n    `SELECT DISTINCT caller_gs.symbol AS caller_symbol, caller_d.relative_path AS caller_file\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents ref_d ON c.document_id = ref_d.id\n    -- Find the enclosing symbol for where the reference appears\n    JOIN defn_enclosing_ranges caller_der\n      ON caller_der.document_id = ref_d.id\n      AND c.start_line >= caller_der.start_line\n      AND c.end_line <= caller_der.end_line\n    JOIN global_symbols caller_gs ON caller_der.symbol_id = caller_gs.id\n    JOIN documents caller_d ON caller_der.document_id = caller_d.id\n    WHERE m.symbol_id = ?\n      AND m.role = 0\n      AND caller_gs.id != ?\n      ${db.symbolNoiseFor('caller_gs')}\n      ${db.pathExclusionsFor('caller_d')}\n    ORDER BY caller_d.relative_path\n    LIMIT 50`,\n    target.symbolId, target.symbolId,\n  );\n\n  // CALLEES: symbols referenced within our target's definition range.\n  const calleeRows = getCalleeRowsForSymbol(db, target, { limit: 50 });\n\n  return {\n    symbol: target.symbol,\n    shortName: shortenSymbol(target.symbol),\n    callers: callerRows\n      .filter((r) => !db.isIgnored(r.caller_file))\n      .map((r) => ({\n        symbol: r.caller_symbol,\n        shortName: shortenSymbol(r.caller_symbol),\n        file: r.caller_file,\n      })),\n    callees: calleeRows\n      .map((r) => ({\n        symbol: r.symbol,\n        shortName: shortenSymbol(r.symbol),\n        file: r.file,\n      })),\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport { findFirstSymbolMatch, getCalleeRowsForSymbol } from '../query-support.js';\nimport type { SimilarSymbolResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find functions with similar callee fingerprints using TF-IDF weighted\n * cosine similarity.\n *\n * Plain Jaccard similarity inflates scores when functions share ubiquitous\n * infrastructure imports (db, types, shortenSymbol). TF-IDF fixes this by\n * weighting each shared callee by how rare it is:\n *\n *   - A callee used by 2 functions (rare) gets high weight → strong signal\n *   - A callee used by 30 functions (common) gets low weight → noise\n *\n * This means two functions sharing `sendWelcomeEmail()` (rare) score\n * much higher than two functions sharing `db.all()` (ubiquitous), even\n * though both are \"shared callees.\"\n */\nexport function similar(\n  db: ScipDatabase,\n  symbolPattern: string,\n  opts: { minSimilarity?: number; limit?: number } = {},\n): SimilarSymbolResult[] {\n  const { minSimilarity = 0.4, limit = 20 } = opts;\n\n  const target = findCallees(db, symbolPattern);\n  if (!target || target.callees.size === 0) return [];\n\n  const candidates = getAllCalleeFingerprints(db, {\n    minCallees: 3,\n    excludeSymbol: target.symbol,\n  });\n\n  // Compute IDF weights across all fingerprints + target\n  const allFingerprints = [target, ...candidates];\n  const idfWeights = computeIdf(allFingerprints);\n\n  const results: SimilarSymbolResult[] = [];\n\n  for (const candidate of candidates) {\n    if (candidate.callees.size < 3) continue;\n\n    const { similarity, significantShared, trivialShared } = weightedSimilarity(\n      target.callees, candidate.callees, idfWeights,\n    );\n\n    if (similarity < minSimilarity) continue;\n    if (significantShared.length < 1) continue; // no real overlap\n\n    results.push({\n      symbolA: target.symbol,\n      shortNameA: shortenSymbol(target.symbol),\n      fileA: target.file,\n      symbolB: candidate.symbol,\n      shortNameB: shortenSymbol(candidate.symbol),\n      fileB: candidate.file,\n      similarity,\n      sharedCallees: significantShared.map(shortenSymbol),\n      uniqueToA: [...difference(target.callees, candidate.callees)].map(shortenSymbol),\n      uniqueToB: [...difference(candidate.callees, target.callees)].map(shortenSymbol),\n    });\n  }\n\n  results.sort((a, b) => b.similarity - a.similarity);\n  return results.slice(0, limit);\n}\n\n/**\n * Find similar symbols across the entire codebase.\n * Uses TF-IDF weighted similarity to filter out infrastructure noise.\n */\nexport function similarAll(\n  db: ScipDatabase,\n  opts: { minSimilarity?: number; limit?: number; scope?: string; minCallees?: number } = {},\n): SimilarSymbolResult[] {\n  const { minSimilarity = 0.5, limit = 20, scope, minCallees = 4 } = opts;\n\n  const all = getAllCalleeFingerprints(db, { minCallees, scope });\n  const idfWeights = computeIdf(all);\n\n  const results: SimilarSymbolResult[] = [];\n\n  for (let i = 0; i < all.length; i++) {\n    for (let j = i + 1; j < all.length; j++) {\n      const a = all[i]!;\n      const b = all[j]!;\n\n      if (a.file === b.file) continue;\n\n      const { similarity, significantShared } = weightedSimilarity(\n        a.callees, b.callees, idfWeights,\n      );\n\n      if (similarity < minSimilarity) continue;\n      if (significantShared.length < 2) continue;\n\n      results.push({\n        symbolA: a.symbol,\n        shortNameA: shortenSymbol(a.symbol),\n        fileA: a.file,\n        symbolB: b.symbol,\n        shortNameB: shortenSymbol(b.symbol),\n        fileB: b.file,\n        similarity,\n        sharedCallees: significantShared.map(shortenSymbol),\n        uniqueToA: [...difference(a.callees, b.callees)].map(shortenSymbol),\n        uniqueToB: [...difference(b.callees, a.callees)].map(shortenSymbol),\n      });\n    }\n\n    if (results.length > limit * 5) break;\n  }\n\n  results.sort((a, b) => b.similarity - a.similarity);\n  return results.slice(0, limit);\n}\n\n// ── TF-IDF Engine ──────────────────────────────────────────\n\n/**\n * Compute inverse document frequency for each callee.\n * IDF(callee) = log(N / df(callee)) where N is total functions\n * and df is how many functions reference that callee.\n *\n * High IDF = rare callee = strong similarity signal.\n * Low IDF = ubiquitous callee = noise.\n */\nfunction computeIdf(fingerprints: SymbolFingerprint[]): Map<string, number> {\n  const n = fingerprints.length;\n  if (n === 0) return new Map();\n\n  // Count how many functions reference each callee\n  const docFreq = new Map<string, number>();\n  for (const fp of fingerprints) {\n    for (const callee of fp.callees) {\n      docFreq.set(callee, (docFreq.get(callee) ?? 0) + 1);\n    }\n  }\n\n  // Compute IDF\n  const idf = new Map<string, number>();\n  for (const [callee, df] of docFreq) {\n    idf.set(callee, Math.log(n / df));\n  }\n\n  return idf;\n}\n\n/**\n * Compute TF-IDF weighted cosine similarity between two callee sets.\n *\n * Each callee is a dimension. Its weight is its IDF score.\n * Cosine similarity of the weighted vectors gives a similarity\n * that ignores ubiquitous callees and emphasizes rare shared ones.\n *\n * Also returns which shared callees are \"significant\" (above-median IDF)\n * vs \"trivial\" (below-median IDF, i.e., infrastructure).\n */\nfunction weightedSimilarity(\n  a: Set<string>,\n  b: Set<string>,\n  idf: Map<string, number>,\n): { similarity: number; significantShared: string[]; trivialShared: string[] } {\n  const shared = intersection(a, b);\n  if (shared.size === 0) return { similarity: 0, significantShared: [], trivialShared: [] };\n\n  // Compute weighted dot product and magnitudes\n  let dotProduct = 0;\n  let magA = 0;\n  let magB = 0;\n\n  const allCallees = new Set([...a, ...b]);\n  for (const callee of allCallees) {\n    const weight = idf.get(callee) ?? 0;\n    const inA = a.has(callee) ? weight : 0;\n    const inB = b.has(callee) ? weight : 0;\n    dotProduct += inA * inB;\n    magA += inA * inA;\n    magB += inB * inB;\n  }\n\n  const magnitude = Math.sqrt(magA) * Math.sqrt(magB);\n  const similarity = magnitude > 0 ? dotProduct / magnitude : 0;\n\n  // Split shared callees into significant (high IDF) and trivial (low IDF)\n  const medianIdf = getMedianIdf(idf);\n  const significantShared: string[] = [];\n  const trivialShared: string[] = [];\n\n  for (const callee of shared) {\n    const weight = idf.get(callee) ?? 0;\n    if (weight >= medianIdf) {\n      significantShared.push(callee);\n    } else {\n      trivialShared.push(callee);\n    }\n  }\n\n  // Sort significant callees by IDF descending (most distinctive first)\n  significantShared.sort((x, y) => (idf.get(y) ?? 0) - (idf.get(x) ?? 0));\n\n  return { similarity, significantShared, trivialShared };\n}\n\nfunction getMedianIdf(idf: Map<string, number>): number {\n  const values = [...idf.values()].sort((a, b) => a - b);\n  if (values.length === 0) return 0;\n  const mid = Math.floor(values.length / 2);\n  return values.length % 2 === 0\n    ? (values[mid - 1]! + values[mid]!) / 2\n    : values[mid]!;\n}\n\n// ── Internal helpers ───────────────────────────────────────\n\ninterface SymbolFingerprint {\n  symbol: string;\n  file: string;\n  callees: Set<string>;\n}\n\nfunction findCallees(\n  db: ScipDatabase,\n  symbolPattern: string,\n): SymbolFingerprint | null {\n  const target = findFirstSymbolMatch(db, symbolPattern);\n\n  if (!target) return null;\n\n  const calleeRows = getCalleeRowsForSymbol(db, target);\n\n  return {\n    symbol: target.symbol,\n    file: target.relativePath,\n    callees: new Set(calleeRows.map((r) => r.symbol)),\n  };\n}\n\nfunction getAllCalleeFingerprints(\n  db: ScipDatabase,\n  opts: { minCallees: number; scope?: string; excludeSymbol?: string },\n): SymbolFingerprint[] {\n  const { minCallees, scope, excludeSymbol } = opts;\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n  const excludeFilter = excludeSymbol ? `AND gs.symbol != '${excludeSymbol.replace(/'/g, \"''\")}'` : '';\n\n  const symbols = db.all<{\n    id: number;\n    symbol: string;\n    document_id: number;\n    start_line: number;\n    end_line: number;\n    relative_path: string;\n  }>(\n    `SELECT gs.id, gs.symbol, der.document_id, der.start_line, der.end_line, d.relative_path\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND (der.end_line - der.start_line + 1) >= 5\n      ${scopeFilter}\n      ${excludeFilter}\n    ORDER BY d.relative_path`,\n  );\n\n  const fingerprints: SymbolFingerprint[] = [];\n\n  for (const sym of symbols) {\n    if (db.isIgnored(sym.relative_path)) continue;\n\n    const calleeRows = getCalleeRowsForSymbol(db, {\n      documentId: sym.document_id,\n      startLine: sym.start_line,\n      endLine: sym.end_line,\n      symbolId: sym.id,\n    });\n\n    const callees = new Set(calleeRows.map((r) => r.symbol));\n    if (callees.size >= minCallees) {\n      fingerprints.push({ symbol: sym.symbol, file: sym.relative_path, callees });\n    }\n  }\n\n  return fingerprints;\n}\n\nfunction intersection<T>(a: Set<T>, b: Set<T>): Set<T> {\n  const result = new Set<T>();\n  for (const item of a) {\n    if (b.has(item)) result.add(item);\n  }\n  return result;\n}\n\nfunction difference<T>(a: Set<T>, b: Set<T>): Set<T> {\n  const result = new Set<T>();\n  for (const item of a) {\n    if (!b.has(item)) result.add(item);\n  }\n  return result;\n}\n","import type { ScipDatabase } from '../db.js';\nimport { buildFileDepGraph } from '../query-support.js';\nimport type { SimilarFileResult } from '../types.js';\n\n/**\n * Find files with similar dependency profiles.\n *\n * Two files that depend on (import from) the same set of other files\n * are structurally doing similar work. High Jaccard similarity between\n * their dependency sets = likely copy-paste variants or consolidation candidates.\n */\nexport function similarFiles(\n  db: ScipDatabase,\n  opts: {\n    minSimilarity?: number;\n    limit?: number;\n    scope?: string;\n    minDeps?: number;\n    filePattern?: string;\n  } = {},\n): SimilarFileResult[] {\n  const { minSimilarity = 0.5, limit = 20, scope, minDeps = 3, filePattern } = opts;\n\n  // Build dependency profile for each file\n  const profiles = buildFileProfiles(db, { scope, minDeps });\n\n  const results: SimilarFileResult[] = [];\n\n  if (filePattern) {\n    // Compare one file against all others\n    const target = profiles.find((p) => p.file.includes(filePattern));\n    if (!target) return [];\n\n    for (const candidate of profiles) {\n      if (candidate.file === target.file) continue;\n      const result = compareProfiles(target, candidate, minSimilarity);\n      if (result) results.push(result);\n    }\n  } else {\n    // Pairwise comparison across all files\n    for (let i = 0; i < profiles.length; i++) {\n      for (let j = i + 1; j < profiles.length; j++) {\n        const result = compareProfiles(profiles[i]!, profiles[j]!, minSimilarity);\n        if (result) results.push(result);\n      }\n      if (results.length > limit * 5) break;\n    }\n  }\n\n  results.sort((a, b) => b.similarity - a.similarity);\n  return results.slice(0, limit);\n}\n\n// ── Internal ───────────────────────────────────────────────\n\ninterface FileProfile {\n  file: string;\n  deps: Set<string>;\n}\n\nfunction buildFileProfiles(\n  db: ScipDatabase,\n  opts: { scope?: string; minDeps: number },\n): FileProfile[] {\n  const { scope, minDeps } = opts;\n  const depMap = buildFileDepGraph(db, scope);\n  const universalDeps = findUniversalDependencies(depMap);\n\n  // Filter to files with enough deps\n  const profiles: FileProfile[] = [];\n  for (const [file, deps] of depMap) {\n    if (deps.size >= minDeps) {\n      profiles.push({\n        file,\n        deps: new Set([...deps].filter((dep) => !universalDeps.has(dep))),\n      });\n    }\n  }\n\n  return profiles;\n}\n\nfunction findUniversalDependencies(\n  depMap: Map<string, Set<string>>,\n): Set<string> {\n  const universalDeps = new Set<string>();\n  const fileCount = depMap.size;\n  if (fileCount === 0) return universalDeps;\n\n  const depCounts = new Map<string, number>();\n  for (const deps of depMap.values()) {\n    for (const dep of deps) {\n      depCounts.set(dep, (depCounts.get(dep) ?? 0) + 1);\n    }\n  }\n\n  for (const [dep, count] of depCounts) {\n    if (count / fileCount > 0.5) {\n      universalDeps.add(dep);\n    }\n  }\n\n  return universalDeps;\n}\n\nfunction compareProfiles(\n  a: FileProfile,\n  b: FileProfile,\n  minSimilarity: number,\n): SimilarFileResult | null {\n  const shared = new Set<string>();\n  for (const dep of a.deps) {\n    if (b.deps.has(dep)) shared.add(dep);\n  }\n\n  if (shared.size === 0) return null;\n\n  const unionSize = new Set([...a.deps, ...b.deps]).size;\n  const similarity = shared.size / unionSize;\n\n  if (similarity < minSimilarity) return null;\n\n  const uniqueA: string[] = [];\n  for (const dep of a.deps) {\n    if (!b.deps.has(dep)) uniqueA.push(dep);\n  }\n  const uniqueB: string[] = [];\n  for (const dep of b.deps) {\n    if (!a.deps.has(dep)) uniqueB.push(dep);\n  }\n\n  return {\n    fileA: a.file,\n    fileB: b.file,\n    similarity,\n    sharedDeps: [...shared],\n    uniqueToA: uniqueA,\n    uniqueToB: uniqueB,\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport { buildFileDepGraph } from '../query-support.js';\nimport type { SimilarChainResult } from '../types.js';\n\n/**\n * Find end-to-end dependency flows that are structurally similar\n * but diverge at a few points — indicating duplicated pipelines\n * that could be consolidated.\n *\n * Uses infrastructure-filtered chain comparison:\n *\n * 1. Build all dependency chains via DFS\n * 2. Compute node frequency across all chains\n * 3. Filter out infrastructure nodes (appearing in >50% of chains)\n * 4. Compare the filtered chains — what's left is the unique pipeline\n * 5. Edit distance on filtered chains finds real structural duplicates\n *\n * Two chains that both pass through db.ts → types.ts is meaningless.\n * Two chains that both pass through userValidation → userRepo → emailService\n * after filtering is a strong consolidation signal.\n */\nexport function similarChains(\n  db: ScipDatabase,\n  opts: {\n    minSimilarity?: number;\n    limit?: number;\n    scope?: string;\n    minChainLength?: number;\n    maxChainLength?: number;\n  } = {},\n): SimilarChainResult[] {\n  const {\n    minSimilarity = 0.5,\n    limit = 15,\n    scope,\n    minChainLength = 3,\n    maxChainLength = 8,\n  } = opts;\n\n  const graph = buildFileDepGraph(db, scope);\n  const rawChains = generateChains(graph, minChainLength, maxChainLength);\n\n  if (rawChains.length === 0) return [];\n\n  // Compute node frequency to identify infrastructure.\n  // Count both general frequency (appears anywhere in chain) and\n  // tail frequency (appears as one of the last 2 nodes). Shared\n  // tails like \"→ db.ts → types.ts\" are infrastructure even if\n  // they don't appear in >50% of chains overall.\n  const nodeFreq = new Map<string, number>();\n  const tailFreq = new Map<string, number>();\n  for (const chain of rawChains) {\n    const seen = new Set<string>();\n    for (const node of chain) {\n      if (!seen.has(node)) {\n        nodeFreq.set(node, (nodeFreq.get(node) ?? 0) + 1);\n        seen.add(node);\n      }\n    }\n    // Track tail nodes (last 2)\n    for (let t = Math.max(0, chain.length - 2); t < chain.length; t++) {\n      tailFreq.set(chain[t]!, (tailFreq.get(chain[t]!) ?? 0) + 1);\n    }\n  }\n\n  // Infrastructure: nodes in >40% of chains OR tail nodes in >30% of chains\n  const infraThreshold = rawChains.length * 0.4;\n  const tailThreshold = rawChains.length * 0.3;\n  const infraNodes = new Set<string>();\n  for (const [node, freq] of nodeFreq) {\n    if (freq > infraThreshold) infraNodes.add(node);\n  }\n  for (const [node, freq] of tailFreq) {\n    if (freq > tailThreshold) infraNodes.add(node);\n  }\n\n  // Also treat structural role files as infrastructure — entry points,\n  // barrels, and orchestrators are not meaningful pipeline nodes.\n  const structuralNames = ['index.ts', 'index.js', 'cli.ts', 'main.ts', 'health.ts', 'health.js'];\n  for (const node of nodeFreq.keys()) {\n    const basename = node.split('/').pop() ?? '';\n    if (structuralNames.includes(basename)) infraNodes.add(node);\n  }\n\n  // Filter chains: remove infrastructure nodes, keep the \"unique pipeline\"\n  const filteredChains: { original: string[]; filtered: string[] }[] = [];\n  for (const chain of rawChains) {\n    const filtered = chain.filter((n) => !infraNodes.has(n));\n    // Only keep chains that have at least 3 non-infrastructure nodes.\n    // Chains with 1-2 unique nodes are just \"query → infra\" which is\n    // the expected pattern, not a consolidation opportunity.\n    if (filtered.length >= 3) {\n      filteredChains.push({ original: chain, filtered });\n    }\n  }\n\n  if (filteredChains.length < 2) return [];\n\n  // Pairwise comparison on filtered chains\n  const results: SimilarChainResult[] = [];\n\n  for (let i = 0; i < filteredChains.length; i++) {\n    for (let j = i + 1; j < filteredChains.length; j++) {\n      const a = filteredChains[i]!;\n      const b = filteredChains[j]!;\n\n      // Quick reject: filtered chains must share at least one non-infra node\n      const setA = new Set(a.filtered);\n      let hasShared = false;\n      for (const node of b.filtered) {\n        if (setA.has(node)) { hasShared = true; break; }\n      }\n      if (!hasShared) continue;\n\n      // Edit distance on the FILTERED chains (infrastructure stripped)\n      const { distance, ops } = editDistance(a.filtered, b.filtered);\n      const maxLen = Math.max(a.filtered.length, b.filtered.length);\n      if (maxLen === 0) continue;\n\n      const similarity = 1 - distance / maxLen;\n      if (similarity < minSimilarity) continue;\n      if (distance === 0) continue; // identical filtered chains = not interesting\n\n      // Divergence points from the filtered comparison\n      const divergencePoints = ops\n        .filter((op) => op.type === 'substitute')\n        .map((op) => ({\n          index: op.indexA,\n          nodeA: a.filtered[op.indexA]!,\n          nodeB: b.filtered[op.indexB]!,\n        }));\n\n      if (divergencePoints.length === 0) continue;\n\n      // Require at least 2 matching (non-divergent) filtered nodes.\n      // A chain pair with 1 match and 1 divergence is just \"two things\n      // that share one dependency\" — not a duplicated pipeline.\n      const matchCount = ops.filter((op) => op.type === 'match').length;\n      if (matchCount < 2) continue;\n\n      // Report using original chains for context, but similarity is from filtered\n      const commonPrefix = getCommonPrefix(a.original, b.original);\n      const commonSuffix = getCommonSuffix(a.original, b.original);\n\n      results.push({\n        chainA: a.original,\n        chainB: b.original,\n        similarity,\n        editDistance: distance,\n        divergencePoints,\n        commonPrefix,\n        commonSuffix,\n      });\n    }\n\n    if (results.length > limit * 10) break;\n  }\n\n  // Sort by similarity desc, then fewest divergence points\n  results.sort((a, b) => {\n    if (Math.abs(b.similarity - a.similarity) > 0.01) return b.similarity - a.similarity;\n    return a.divergencePoints.length - b.divergencePoints.length;\n  });\n\n  // Deduplicate sub-chains\n  const deduped: SimilarChainResult[] = [];\n  for (const r of results) {\n    const isDuplicate = deduped.some(\n      (existing) =>\n        isSubChain(r.chainA, existing.chainA) && isSubChain(r.chainB, existing.chainB),\n    );\n    if (!isDuplicate) deduped.push(r);\n    if (deduped.length >= limit) break;\n  }\n\n  return deduped;\n}\n\n// ── Chain generation ───────────────────────────────────────\n\nfunction generateChains(\n  graph: Map<string, Set<string>>,\n  minLen: number,\n  maxLen: number,\n): string[][] {\n  const chains: string[][] = [];\n  const maxChains = 500;\n\n  for (const startNode of graph.keys()) {\n    if (chains.length >= maxChains) break;\n    dfsChains(graph, startNode, [startNode], new Set([startNode]), minLen, maxLen, chains, maxChains);\n  }\n\n  return chains;\n}\n\nfunction dfsChains(\n  graph: Map<string, Set<string>>,\n  node: string,\n  path: string[],\n  visited: Set<string>,\n  minLen: number,\n  maxLen: number,\n  results: string[][],\n  maxResults: number,\n): void {\n  if (results.length >= maxResults) return;\n  if (path.length >= maxLen) {\n    if (path.length >= minLen) results.push([...path]);\n    return;\n  }\n\n  const neighbors = graph.get(node);\n  if (!neighbors || neighbors.size === 0) {\n    if (path.length >= minLen) results.push([...path]);\n    return;\n  }\n\n  let extended = false;\n  for (const next of neighbors) {\n    if (visited.has(next)) continue;\n    visited.add(next);\n    path.push(next);\n    dfsChains(graph, next, path, visited, minLen, maxLen, results, maxResults);\n    path.pop();\n    visited.delete(next);\n    extended = true;\n    if (results.length >= maxResults) return;\n  }\n\n  if (!extended && path.length >= minLen) {\n    results.push([...path]);\n  }\n}\n\n// ── Edit distance ──────────────────────────────────────────\n\ninterface EditOp {\n  type: 'match' | 'substitute' | 'insert' | 'delete';\n  indexA: number;\n  indexB: number;\n}\n\nfunction editDistance(a: string[], b: string[]): { distance: number; ops: EditOp[] } {\n  const m = a.length;\n  const n = b.length;\n\n  const dp: number[][] = Array.from({ length: m + 1 }, () => Array(n + 1).fill(0));\n  for (let i = 0; i <= m; i++) dp[i]![0] = i;\n  for (let j = 0; j <= n; j++) dp[0]![j] = j;\n\n  for (let i = 1; i <= m; i++) {\n    for (let j = 1; j <= n; j++) {\n      if (a[i - 1] === b[j - 1]) {\n        dp[i]![j] = dp[i - 1]![j - 1]!;\n      } else {\n        dp[i]![j] = 1 + Math.min(\n          dp[i - 1]![j]!,\n          dp[i]![j - 1]!,\n          dp[i - 1]![j - 1]!,\n        );\n      }\n    }\n  }\n\n  const ops: EditOp[] = [];\n  let i = m, j = n;\n  while (i > 0 || j > 0) {\n    if (i > 0 && j > 0 && a[i - 1] === b[j - 1]) {\n      ops.unshift({ type: 'match', indexA: i - 1, indexB: j - 1 });\n      i--; j--;\n    } else if (i > 0 && j > 0 && dp[i]![j] === dp[i - 1]![j - 1]! + 1) {\n      ops.unshift({ type: 'substitute', indexA: i - 1, indexB: j - 1 });\n      i--; j--;\n    } else if (j > 0 && dp[i]![j] === dp[i]![j - 1]! + 1) {\n      ops.unshift({ type: 'insert', indexA: i, indexB: j - 1 });\n      j--;\n    } else {\n      ops.unshift({ type: 'delete', indexA: i - 1, indexB: j });\n      i--;\n    }\n  }\n\n  return { distance: dp[m]![n]!, ops };\n}\n\n// ── Utility ────────────────────────────────────────────────\n\nfunction getCommonPrefix(a: string[], b: string[]): string[] {\n  const prefix: string[] = [];\n  for (let i = 0; i < Math.min(a.length, b.length); i++) {\n    if (a[i] === b[i]) prefix.push(a[i]!);\n    else break;\n  }\n  return prefix;\n}\n\nfunction getCommonSuffix(a: string[], b: string[]): string[] {\n  const suffix: string[] = [];\n  let ai = a.length - 1;\n  let bi = b.length - 1;\n  while (ai >= 0 && bi >= 0 && a[ai] === b[bi]) {\n    suffix.unshift(a[ai]!);\n    ai--; bi--;\n  }\n  return suffix;\n}\n\nfunction isSubChain(sub: string[], full: string[]): boolean {\n  if (sub.length > full.length) return false;\n  const fullStr = full.join('→');\n  const subStr = sub.join('→');\n  return fullStr.includes(subStr);\n}\n","import type { ScipDatabase } from '../db.js';\nimport { getCalleeRowsForSymbol } from '../query-support.js';\nimport type { ExtractCandidate } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find functions with natural extraction seams.\n *\n * A large function that references two distinct groups of symbols —\n * where group A's symbols are never co-referenced with group B's —\n * has a natural extraction boundary. The isolated cluster can likely\n * be pulled into its own function.\n *\n * We detect this by:\n * 1. Finding all callees of a function\n * 2. Building a co-occurrence graph (which callees appear in the same chunk)\n * 3. Finding connected components — disconnected components = extraction seams\n * 4. Scoring each cluster by how isolated it is from the rest\n */\nexport function extractCandidates(\n  db: ScipDatabase,\n  opts: { scope?: string; minLoc?: number; minCallees?: number; limit?: number } = {},\n): ExtractCandidate[] {\n  const { scope, minLoc = 10, minCallees = 6, limit = 20 } = opts;\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  // Find functions large enough to consider\n  const symbols = db.all<{\n    id: number;\n    symbol: string;\n    document_id: number;\n    start_line: number;\n    end_line: number;\n    relative_path: string;\n  }>(\n    `SELECT gs.id, gs.symbol, der.document_id, der.start_line, der.end_line, d.relative_path\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND (der.end_line - der.start_line + 1) >= ?\n      ${scopeFilter}\n    ORDER BY (der.end_line - der.start_line + 1) DESC`,\n    minLoc,\n  );\n\n  const results: ExtractCandidate[] = [];\n\n  for (const sym of symbols) {\n    if (db.isIgnored(sym.relative_path)) continue;\n\n    // Skip pure type files — \"callees\" in a type file are just type references,\n    // not function calls. Splitting type files is a cosmetic choice, not an\n    // extraction opportunity.\n    const basename = sym.relative_path.split('/').pop() ?? '';\n    if (basename.includes('types')) continue;\n\n    // Get callees with their chunk locations (to build co-occurrence)\n    const calleeChunks = getCalleeRowsForSymbol(db, {\n      documentId: sym.document_id,\n      startLine: sym.start_line,\n      endLine: sym.end_line,\n      symbolId: sym.id,\n    });\n\n    // Collect unique callees\n    const calleeSet = new Set(calleeChunks.map((c) => c.symbol));\n    if (calleeSet.size < minCallees) continue;\n\n    // Build co-occurrence graph: two callees are connected if they\n    // appear in the same chunk (meaning they're used in proximity)\n    const cooccurrence = new Map<string, Set<string>>();\n    for (const callee of calleeSet) {\n      cooccurrence.set(callee, new Set());\n    }\n\n    // Group by chunk\n    const chunkToCallees = new Map<number, Set<string>>();\n    for (const cc of calleeChunks) {\n      if (!chunkToCallees.has(cc.chunkId)) chunkToCallees.set(cc.chunkId, new Set());\n      chunkToCallees.get(cc.chunkId)!.add(cc.symbol);\n    }\n\n    // Callees in the same chunk are co-occurring\n    for (const callees of chunkToCallees.values()) {\n      const arr = [...callees];\n      for (let i = 0; i < arr.length; i++) {\n        for (let j = i + 1; j < arr.length; j++) {\n          cooccurrence.get(arr[i]!)!.add(arr[j]!);\n          cooccurrence.get(arr[j]!)!.add(arr[i]!);\n        }\n      }\n    }\n\n    // Find connected components via BFS\n    const visited = new Set<string>();\n    const clusters: Set<string>[] = [];\n\n    for (const callee of calleeSet) {\n      if (visited.has(callee)) continue;\n      const cluster = new Set<string>();\n      const queue = [callee];\n      while (queue.length > 0) {\n        const current = queue.pop()!;\n        if (visited.has(current)) continue;\n        visited.add(current);\n        cluster.add(current);\n        for (const neighbor of cooccurrence.get(current) ?? []) {\n          if (!visited.has(neighbor)) queue.push(neighbor);\n        }\n      }\n      clusters.push(cluster);\n    }\n\n    // Only interesting if there are multiple clusters (= extraction seams exist)\n    if (clusters.length < 2) continue;\n\n    // Score each cluster by isolation:\n    // isolation = 1 - (edges to other clusters / total possible edges to other clusters)\n    const scoredClusters = clusters\n      .filter((c) => c.size >= 2) // single-callee clusters aren't interesting\n      .map((cluster) => {\n        const otherCallees = new Set<string>();\n        for (const c of clusters) {\n          if (c !== cluster) {\n            for (const s of c) otherCallees.add(s);\n          }\n        }\n\n        // Count cross-cluster edges\n        let crossEdges = 0;\n        for (const callee of cluster) {\n          for (const neighbor of cooccurrence.get(callee) ?? []) {\n            if (otherCallees.has(neighbor)) crossEdges++;\n          }\n        }\n\n        const maxCrossEdges = cluster.size * otherCallees.size;\n        const isolation = maxCrossEdges > 0 ? 1 - crossEdges / maxCrossEdges : 1;\n\n        return {\n          callees: [...cluster].map(shortenSymbol),\n          isolation,\n        };\n      })\n      .filter((c) => c.isolation > 0.5) // Only report well-isolated clusters\n      .sort((a, b) => b.isolation - a.isolation);\n\n    if (scoredClusters.length > 0) {\n      results.push({\n        symbol: sym.symbol,\n        shortName: shortenSymbol(sym.symbol),\n        relativePath: sym.relative_path,\n        startLine: sym.start_line,\n        endLine: sym.end_line,\n        loc: sym.end_line - sym.start_line + 1,\n        totalCallees: calleeSet.size,\n        clusters: scoredClusters,\n      });\n    }\n  }\n\n  results.sort((a, b) => b.clusters.length - a.clusters.length || b.loc - a.loc);\n  return results.slice(0, limit);\n}\n","import type { ScipDatabase } from '../db.js';\nimport { findFirstSymbolMatch } from '../query-support.js';\nimport type { AffectedResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Full transitive closure of symbols that could break if a given symbol changes.\n * BFS from the target through the mention graph: depth 1 = direct consumers,\n * depth 2 = consumers of consumers, etc.\n */\nexport function affected(\n  db: ScipDatabase,\n  symbolPattern: string,\n  opts: { maxDepth?: number; scope?: string } = {},\n): AffectedResult[] {\n  const { maxDepth = 5, scope } = opts;\n\n  const target = findFirstSymbolMatch(db, symbolPattern);\n  if (!target) return [];\n\n  const scopeFilter = scope\n    ? `AND enc_d.relative_path LIKE '%${scope}%'`\n    : '';\n\n  const results: AffectedResult[] = [];\n  const visited = new Set<number>([target.symbolId]);\n  let frontier = new Set<number>([target.symbolId]);\n\n  for (let depth = 1; depth <= maxDepth; depth++) {\n    if (frontier.size === 0) break;\n\n    const placeholders = [...frontier].map(() => '?').join(',');\n    const nextFrontier = new Set<number>();\n\n    // For each symbol in the frontier, find enclosing symbols whose\n    // definition ranges contain a reference (role=0) to that frontier symbol.\n    const rows = db.all<{\n      symbol_id: number;\n      symbol: string;\n      relative_path: string;\n    }>(\n      `SELECT DISTINCT\n        enc_gs.id AS symbol_id,\n        enc_gs.symbol AS symbol,\n        enc_d.relative_path AS relative_path\n      FROM mentions m\n      JOIN chunks c ON m.chunk_id = c.id\n      JOIN documents ref_d ON c.document_id = ref_d.id\n      JOIN defn_enclosing_ranges enc_der\n        ON enc_der.document_id = ref_d.id\n        AND c.start_line >= enc_der.start_line\n        AND c.end_line <= enc_der.end_line\n      JOIN global_symbols enc_gs ON enc_der.symbol_id = enc_gs.id\n      JOIN documents enc_d ON enc_der.document_id = enc_d.id\n      WHERE m.symbol_id IN (${placeholders})\n        AND m.role = 0\n        AND enc_gs.id NOT IN (${placeholders})\n        ${db.symbolNoiseFor('enc_gs')}\n        ${db.pathExclusionsFor('enc_d')}\n        ${scopeFilter}`,\n      ...[...frontier],\n      ...[...frontier],\n    );\n\n    for (const row of rows) {\n      if (visited.has(row.symbol_id)) continue;\n      if (db.isIgnored(row.relative_path)) continue;\n\n      visited.add(row.symbol_id);\n      nextFrontier.add(row.symbol_id);\n\n      results.push({\n        symbol: row.symbol,\n        shortName: shortenSymbol(row.symbol),\n        file: row.relative_path,\n        depth,\n      });\n    }\n\n    frontier = nextFrontier;\n  }\n\n  // Sort by depth then file path\n  results.sort((a, b) => a.depth - b.depth || a.file.localeCompare(b.file));\n  return results;\n}\n","import type { ScipDatabase } from '../db.js';\nimport { TEST_FILE_PATTERNS, testFileMatchSql } from '../query-support.js';\nimport type { ChangeSurfaceEntry, ChangeSurfaceResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Pre-change briefing for a file. For each symbol defined in the file,\n * reports external consumer count, test coverage, and risk level.\n */\nexport function changeSurface(\n  db: ScipDatabase,\n  filePattern: string,\n): ChangeSurfaceResult | null {\n  // Find the file\n  const doc = db.get<{ id: number; relative_path: string }>(\n    `SELECT id, relative_path FROM documents\n     WHERE relative_path LIKE ?\n       ${db.pathExclusionsFor('documents')}\n     LIMIT 1`,\n    `%${filePattern}%`,\n  );\n\n  if (!doc || db.isIgnored(doc.relative_path)) return null;\n\n  // Get all symbols defined in this file, excluding typeLiterals\n  const syms = db.all<{\n    symbol_id: number;\n    symbol: string;\n    start_line: number;\n    end_line: number;\n  }>(\n    `SELECT DISTINCT gs.id AS symbol_id, gs.symbol, der.start_line, der.end_line\n    FROM defn_enclosing_ranges der\n    JOIN global_symbols gs ON der.symbol_id = gs.id\n    WHERE der.document_id = ?\n      ${db.symbolNoiseFor('gs')}\n    ORDER BY der.start_line`,\n    doc.id,\n  );\n\n  const testPatternSql = testFileMatchSql('ref_d', TEST_FILE_PATTERNS);\n\n  const symbols: ChangeSurfaceEntry[] = [];\n  let totalExternalConsumers = 0;\n  let coveredCount = 0;\n\n  for (const sym of syms) {\n    // Count external consumers: mentions with role=0 from different documents\n    const consumerRow = db.get<{ consumer_count: number }>(\n      `SELECT COUNT(DISTINCT c.document_id) AS consumer_count\n      FROM mentions m\n      JOIN chunks c ON m.chunk_id = c.id\n      WHERE m.symbol_id = ?\n        AND m.role = 0\n        AND c.document_id != ?`,\n      sym.symbol_id,\n      doc.id,\n    );\n\n    const externalConsumers = consumerRow?.consumer_count ?? 0;\n\n    // Find test files that reference this symbol\n    const testFiles = db.all<{ relative_path: string }>(\n      `SELECT DISTINCT ref_d.relative_path\n      FROM mentions m\n      JOIN chunks c ON m.chunk_id = c.id\n      JOIN documents ref_d ON c.document_id = ref_d.id\n      WHERE m.symbol_id = ?\n        AND m.role = 0\n        AND (${testPatternSql})\n      ORDER BY ref_d.relative_path`,\n      sym.symbol_id,\n    ).map((r) => r.relative_path);\n\n    const hasTests = testFiles.length > 0;\n    if (hasTests) coveredCount++;\n\n    // Risk level determination\n    let riskLevel: 'low' | 'medium' | 'high';\n    if (externalConsumers > 10 && !hasTests) {\n      riskLevel = 'high';\n    } else if (externalConsumers > 5 || !hasTests) {\n      riskLevel = 'medium';\n    } else {\n      riskLevel = 'low';\n    }\n\n    totalExternalConsumers += externalConsumers;\n\n    symbols.push({\n      symbol: sym.symbol,\n      shortName: shortenSymbol(sym.symbol),\n      startLine: sym.start_line,\n      endLine: sym.end_line,\n      externalConsumers,\n      testFiles,\n      riskLevel,\n    });\n  }\n\n  const testCoveragePercent =\n    symbols.length > 0 ? Math.round((coveredCount / symbols.length) * 100) : 0;\n\n  return {\n    file: doc.relative_path,\n    symbols,\n    totalExternalConsumers,\n    testCoveragePercent,\n  };\n}\n","import { execFileSync } from 'node:child_process';\nimport type { ScipDatabase } from '../db.js';\nimport { TEST_FILE_PATTERNS, testFileMatchSql } from '../query-support.js';\nimport type { DiffImpactResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Given a git diff, compute the affected symbol set.\n * Finds all symbols defined in changed files, their fan-in,\n * the files that consume them, and test coverage gaps.\n */\nexport function diffImpact(\n  db: ScipDatabase,\n  opts: { base?: string } = {},\n): DiffImpactResult {\n  const { base = 'HEAD' } = opts;\n\n  // Get changed files from git\n  let changedFileLines: string[];\n  try {\n    const stdout = execFileSync('git', ['diff', '--name-only', base], {\n      encoding: 'utf-8',\n      cwd: db.config.projectRoot,\n      timeout: 10_000,\n    });\n    changedFileLines = stdout\n      .split('\\n')\n      .map((l) => l.trim())\n      .filter((l) => l.length > 0);\n  } catch {\n    // Not in a git repo or git not available — return empty result\n    return {\n      changedFiles: [],\n      changedSymbols: [],\n      affectedConsumers: [],\n      uncoveredSymbols: [],\n      summary: {\n        totalChangedFiles: 0,\n        totalChangedSymbols: 0,\n        totalAffectedFiles: 0,\n        testCoveragePercent: 0,\n      },\n    };\n  }\n\n  if (changedFileLines.length === 0) {\n    return {\n      changedFiles: [],\n      changedSymbols: [],\n      affectedConsumers: [],\n      uncoveredSymbols: [],\n      summary: {\n        totalChangedFiles: 0,\n        totalChangedSymbols: 0,\n        totalAffectedFiles: 0,\n        testCoveragePercent: 0,\n      },\n    };\n  }\n\n  // Match changed files against the index\n  const changedFiles: string[] = [];\n  const changedDocIds: number[] = [];\n\n  for (const file of changedFileLines) {\n    const doc = db.get<{ id: number; relative_path: string }>(\n      `SELECT id, relative_path FROM documents\n       WHERE relative_path LIKE ?\n       LIMIT 1`,\n      `%${file}`,\n    );\n    if (doc && !db.isIgnored(doc.relative_path)) {\n      changedFiles.push(doc.relative_path);\n      changedDocIds.push(doc.id);\n    }\n  }\n\n  if (changedDocIds.length === 0) {\n    return {\n      changedFiles: changedFileLines,\n      changedSymbols: [],\n      affectedConsumers: [],\n      uncoveredSymbols: [],\n      summary: {\n        totalChangedFiles: changedFileLines.length,\n        totalChangedSymbols: 0,\n        totalAffectedFiles: 0,\n        testCoveragePercent: 0,\n      },\n    };\n  }\n\n  // Get all symbols defined in changed files\n  const docPlaceholders = changedDocIds.map(() => '?').join(',');\n  const syms = db.all<{\n    symbol_id: number;\n    symbol: string;\n    relative_path: string;\n  }>(\n    `SELECT DISTINCT gs.id AS symbol_id, gs.symbol, d.relative_path\n    FROM defn_enclosing_ranges der\n    JOIN global_symbols gs ON der.symbol_id = gs.id\n    JOIN documents d ON der.document_id = d.id\n    WHERE der.document_id IN (${docPlaceholders})\n      ${db.symbolNoiseFor('gs')}\n    ORDER BY d.relative_path`,\n    ...changedDocIds,\n  );\n\n  // For each symbol, compute fan-in (distinct referencing documents)\n  const testPatternSql = testFileMatchSql('ref_d', TEST_FILE_PATTERNS);\n  const changedSymbols: DiffImpactResult['changedSymbols'] = [];\n  const consumerMap = new Map<string, Set<string>>(); // file -> set of consumed symbol shortNames\n  const uncoveredSymbols: DiffImpactResult['uncoveredSymbols'] = [];\n  let coveredCount = 0;\n\n  for (const sym of syms) {\n    // Fan-in: distinct files that reference this symbol\n    const fanInRow = db.get<{ fan_in: number }>(\n      `SELECT COUNT(DISTINCT c.document_id) AS fan_in\n      FROM mentions m\n      JOIN chunks c ON m.chunk_id = c.id\n      WHERE m.symbol_id = ?\n        AND m.role = 0`,\n      sym.symbol_id,\n    );\n\n    const fanIn = fanInRow?.fan_in ?? 0;\n    const shortName = shortenSymbol(sym.symbol);\n\n    changedSymbols.push({\n      symbol: sym.symbol,\n      shortName,\n      file: sym.relative_path,\n      fanIn,\n    });\n\n    // Collect consumer files (excluding the changed files themselves)\n    const consumers = db.all<{ relative_path: string }>(\n      `SELECT DISTINCT ref_d.relative_path\n      FROM mentions m\n      JOIN chunks c ON m.chunk_id = c.id\n      JOIN documents ref_d ON c.document_id = ref_d.id\n      WHERE m.symbol_id = ?\n        AND m.role = 0\n        AND ref_d.relative_path NOT IN (${changedFiles.map(() => '?').join(',')})\n        ${db.pathExclusionsFor('ref_d')}`,\n      sym.symbol_id,\n      ...changedFiles,\n    );\n\n    for (const consumer of consumers) {\n      if (db.isIgnored(consumer.relative_path)) continue;\n      if (!consumerMap.has(consumer.relative_path)) {\n        consumerMap.set(consumer.relative_path, new Set());\n      }\n      consumerMap.get(consumer.relative_path)!.add(shortName);\n    }\n\n    // Check test coverage\n    const hasTest = db.get<{ c: number }>(\n      `SELECT COUNT(*) AS c\n      FROM mentions m\n      JOIN chunks c ON m.chunk_id = c.id\n      JOIN documents ref_d ON c.document_id = ref_d.id\n      WHERE m.symbol_id = ?\n        AND m.role = 0\n        AND (${testPatternSql})`,\n      sym.symbol_id,\n    );\n\n    if (hasTest && hasTest.c > 0) {\n      coveredCount++;\n    } else {\n      uncoveredSymbols.push({\n        symbol: sym.symbol,\n        shortName,\n        file: sym.relative_path,\n      });\n    }\n  }\n\n  // Build affected consumers list\n  const affectedConsumers = [...consumerMap.entries()]\n    .map(([file, symbols]) => ({ file, consumedSymbols: symbols.size }))\n    .sort((a, b) => b.consumedSymbols - a.consumedSymbols);\n\n  const totalSymbols = changedSymbols.length;\n  const testCoveragePercent =\n    totalSymbols > 0 ? Math.round((coveredCount / totalSymbols) * 100) : 0;\n\n  return {\n    changedFiles,\n    changedSymbols,\n    affectedConsumers,\n    uncoveredSymbols,\n    summary: {\n      totalChangedFiles: changedFiles.length,\n      totalChangedSymbols: totalSymbols,\n      totalAffectedFiles: affectedConsumers.length,\n      testCoveragePercent,\n    },\n  };\n}\n","import path from 'node:path';\nimport type { ScipDatabase } from '../db.js';\nimport { buildFileDepGraph } from '../query-support.js';\nimport type { DriftResult, DriftSummary } from '../types.js';\n\n/**\n * Detect structural drift using the reference graph, not just import patterns.\n *\n * Three types of drift, each detecting a real problem:\n *\n * 1. **Unused imports** — file depends on a module but never references\n *    any of its symbols. Dead dependency, safe to remove.\n *\n * 2. **Layer violations** — file imports from a directory it shouldn't\n *    based on the project's directory structure (e.g., a query importing\n *    from reindex, a helper importing from CLI). Architectural decay.\n *\n * 3. **Pattern deviations** — file imports something no sibling does,\n *    suggesting it's reaching outside its expected scope. Only flagged\n *    when the file is the ONLY one in its directory with that dep.\n */\nexport function drift(\n  db: ScipDatabase,\n  opts?: { scope?: string; minDeviation?: number },\n): DriftSummary {\n  const { scope } = opts ?? {};\n\n  // Build file dep graph (which files depend on which)\n  const depGraph = buildFileDepGraph(db, scope);\n\n  // Build symbol-level reference graph: for each file, which other files'\n  // symbols does it actually reference?\n  const symbolRefs = buildSymbolRefGraph(db, scope);\n\n  const results: DriftResult[] = [];\n\n  // ── Angle 1: Unused imports ──────────────────────────────\n  // File depends on module B (via dep graph) but never references\n  // any symbol defined in B (via symbol ref graph).\n  for (const [file, deps] of depGraph) {\n    if (isStructuralRole(path.basename(file))) continue;\n\n    const referencedFiles = symbolRefs.get(file) ?? new Set<string>();\n\n    for (const dep of deps) {\n      if (!referencedFiles.has(dep)) {\n        // This file \"depends on\" dep but never references its symbols.\n        // This can happen when the dep is imported for types only\n        // (which don't appear in the mention graph). Skip type-heavy deps.\n        if (isLikelyTypeOnlyDep(dep)) continue;\n\n        results.push({\n          file,\n          kind: 'unused-import',\n          description: `Depends on ${dep} but references none of its symbols`,\n          dep,\n        });\n      }\n    }\n  }\n\n  // ── Angle 2: Layer violations ────────────────────────────\n  // Detect when a file imports from a directory that represents\n  // a different architectural layer. We infer layers from the\n  // directory structure: files in the same top-level dir are peers,\n  // files in different top-level dirs crossing inward is a violation.\n  const layerRules = inferLayerRules(depGraph);\n\n  for (const [file, deps] of depGraph) {\n    if (isStructuralRole(path.basename(file))) continue;\n\n    const fileLayer = getTopDir(file);\n    for (const dep of deps) {\n      const depLayer = getTopDir(dep);\n      if (fileLayer === depLayer) continue; // same layer, fine\n\n      const violation = layerRules.get(`${fileLayer}->${depLayer}`);\n      if (violation === 'violation') {\n        results.push({\n          file,\n          kind: 'layer-violation',\n          description: `Imports from ${depLayer}/ (${dep}) — may cross architectural boundary`,\n          dep,\n          detail: `${fileLayer}/ should not depend on ${depLayer}/`,\n        });\n      }\n    }\n  }\n\n  // ── Angle 3: Unique deps (pattern deviation) ─────────────\n  // If a file is the ONLY one in its directory that depends on a\n  // particular module, that dependency is unusual and worth flagging.\n  const dirToFiles = new Map<string, string[]>();\n  for (const file of depGraph.keys()) {\n    const dir = path.dirname(file);\n    if (!dirToFiles.has(dir)) dirToFiles.set(dir, []);\n    dirToFiles.get(dir)!.push(file);\n  }\n\n  for (const [dir, files] of dirToFiles) {\n    if (files.length < 3) continue;\n\n    // Count dep frequency across siblings\n    const depFreq = new Map<string, number>();\n    for (const file of files) {\n      if (isStructuralRole(path.basename(file))) continue;\n      for (const dep of depGraph.get(file) ?? []) {\n        depFreq.set(dep, (depFreq.get(dep) ?? 0) + 1);\n      }\n    }\n\n    for (const file of files) {\n      if (isStructuralRole(path.basename(file))) continue;\n      for (const dep of depGraph.get(file) ?? []) {\n        if ((depFreq.get(dep) ?? 0) === 1) {\n          // This file is the only one in its dir that depends on this module\n          // Skip if dep is in the same directory (sibling imports are normal)\n          if (path.dirname(dep) === dir) continue;\n\n          results.push({\n            file,\n            kind: 'pattern-deviation',\n            description: `Only file in ${dir}/ that depends on ${dep}`,\n            dep,\n          });\n        }\n      }\n    }\n  }\n\n  return {\n    results,\n    unusedImports: results.filter((r) => r.kind === 'unused-import').length,\n    layerViolations: results.filter((r) => r.kind === 'layer-violation').length,\n    patternDeviations: results.filter((r) => r.kind === 'pattern-deviation').length,\n  };\n}\n\n// ── Helpers ────────────────────────────────────────────────\n\n/**\n * Build a map of file → set of files whose symbols it references.\n * This is more precise than the dep graph because it uses actual\n * symbol mentions, not just import statements.\n */\nfunction buildSymbolRefGraph(\n  db: ScipDatabase,\n  scope?: string,\n): Map<string, Set<string>> {\n  const scopeFilter = scope ? `AND d1.relative_path LIKE '%${scope}%'` : '';\n\n  const rows = db.all<{ from_file: string; to_file: string }>(\n    `SELECT DISTINCT d1.relative_path AS from_file, d2.relative_path AS to_file\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d1 ON c.document_id = d1.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d2 ON der.document_id = d2.id\n    WHERE d1.id != d2.id\n      AND m.role = 0\n      ${db.pathExclusionsFor('d1', 'd2')}\n      ${scopeFilter}`,\n  );\n\n  const graph = new Map<string, Set<string>>();\n  for (const r of rows) {\n    if (db.isIgnored(r.from_file) || db.isIgnored(r.to_file)) continue;\n    if (!graph.has(r.from_file)) graph.set(r.from_file, new Set());\n    graph.get(r.from_file)!.add(r.to_file);\n  }\n  return graph;\n}\n\n/**\n * Infer layer boundary rules from the dependency graph.\n * If directory A never depends on directory B across the entire codebase,\n * then a new A→B dependency is a violation.\n */\nfunction inferLayerRules(\n  depGraph: Map<string, Set<string>>,\n): Map<string, 'ok' | 'violation'> {\n  const layerEdges = new Map<string, number>();\n  const layerSet = new Set<string>();\n\n  for (const [file, deps] of depGraph) {\n    const fromLayer = getTopDir(file);\n    layerSet.add(fromLayer);\n    for (const dep of deps) {\n      const toLayer = getTopDir(dep);\n      if (fromLayer === toLayer) continue;\n      layerSet.add(toLayer);\n      const key = `${fromLayer}->${toLayer}`;\n      layerEdges.set(key, (layerEdges.get(key) ?? 0) + 1);\n    }\n  }\n\n  // An edge that appears only 1-2 times across the whole codebase\n  // is likely a violation (anomalous cross-layer dep).\n  // Edges that appear many times are established patterns.\n  const rules = new Map<string, 'ok' | 'violation'>();\n  for (const [edge, count] of layerEdges) {\n    rules.set(edge, count <= 2 ? 'violation' : 'ok');\n  }\n\n  return rules;\n}\n\nfunction getTopDir(filePath: string): string {\n  const parts = filePath.split('/');\n  return parts[0] ?? filePath;\n}\n\nfunction isLikelyTypeOnlyDep(dep: string): boolean {\n  return dep.includes('types') || dep.endsWith('.d.ts');\n}\n\nfunction isStructuralRole(basename: string): boolean {\n  if (basename === 'index.ts' || basename === 'index.js') return true;\n  if (basename === 'cli.ts' || basename === 'main.ts' || basename === 'main.rs') return true;\n  if (basename.includes('worker.') || basename.includes('postinstall.')) return true;\n  if (basename === 'health.ts' || basename === 'health.js') return true;\n  return false;\n}\n","import type { ScipDatabase } from '../db.js';\nimport { testFileExclusionSql } from '../query-support.js';\nimport type { WrapperCandidate } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find wrapper candidates: symbols called by only one other symbol.\n *\n * These are premature abstractions that add indirection without\n * providing reuse. A function with fan-in = 1 whose sole caller\n * is widely used is a strong signal of unnecessary wrapping.\n */\nexport function wrapperCandidates(\n  db: ScipDatabase,\n  opts?: { scope?: string; maxLoc?: number; limit?: number },\n): WrapperCandidate[] {\n  const { scope, maxLoc = 15, limit = 30 } = opts ?? {};\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  // Find all symbols with exactly 1 cross-file consumer (fan-in = 1),\n  // along with who that single caller is and the caller's own fan-in.\n  const rows = db.all<{\n    symbol: string;\n    file: string;\n    start_line: number;\n    end_line: number;\n    loc: number;\n    caller_symbol: string;\n    caller_fan_in: number;\n  }>(\n    `SELECT * FROM (\n      SELECT\n        gs.symbol,\n        d.relative_path AS file,\n        der.start_line,\n        der.end_line,\n        (der.end_line - der.start_line + 1) AS loc,\n        -- The single caller: the symbol whose definition range contains\n        -- the chunk that references our target\n        (SELECT caller_gs.symbol\n         FROM mentions ref_m\n         JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n         JOIN defn_enclosing_ranges caller_der\n           ON caller_der.document_id = ref_c.document_id\n           AND ref_c.start_line >= caller_der.start_line\n           AND ref_c.end_line <= caller_der.end_line\n         JOIN global_symbols caller_gs ON caller_der.symbol_id = caller_gs.id\n         WHERE ref_m.symbol_id = gs.id\n           AND ref_m.role = 0\n           AND ref_c.document_id != der.document_id\n         LIMIT 1\n        ) AS caller_symbol,\n        -- Fan-in of that single caller\n        (SELECT COUNT(DISTINCT caller_ref_c.document_id)\n         FROM mentions caller_ref_m\n         JOIN chunks caller_ref_c ON caller_ref_m.chunk_id = caller_ref_c.id\n         WHERE caller_ref_m.symbol_id = (\n           SELECT caller_der2.symbol_id\n           FROM mentions ref_m2\n           JOIN chunks ref_c2 ON ref_m2.chunk_id = ref_c2.id\n           JOIN defn_enclosing_ranges caller_der2\n             ON caller_der2.document_id = ref_c2.document_id\n             AND ref_c2.start_line >= caller_der2.start_line\n             AND ref_c2.end_line <= caller_der2.end_line\n           WHERE ref_m2.symbol_id = gs.id\n             AND ref_m2.role = 0\n             AND ref_c2.document_id != der.document_id\n           LIMIT 1\n         )\n         AND caller_ref_m.role = 0\n        ) AS caller_fan_in\n      FROM global_symbols gs\n      JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n      JOIN documents d ON der.document_id = d.id\n      WHERE 1 = 1\n        ${db.pathExclusionsFor('d')}\n        AND ${testFileExclusionSql('d')}\n        ${db.symbolNoiseFor('gs')}\n        -- Only functions/terms, not type definitions (types with # are not wrappers)\n        AND gs.symbol NOT LIKE '%#'\n        AND (der.end_line - der.start_line + 1) <= ?\n        AND (der.end_line - der.start_line + 1) >= 2\n        ${scopeFilter}\n        -- Exactly 1 cross-file consumer\n        AND (\n          SELECT COUNT(DISTINCT ref_c.document_id)\n          FROM mentions ref_m\n          JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n          WHERE ref_m.symbol_id = gs.id\n            AND ref_m.role = 0\n            AND ref_c.document_id != der.document_id\n        ) = 1\n    ) WHERE caller_symbol IS NOT NULL AND caller_fan_in > 3\n    ORDER BY caller_fan_in DESC, loc DESC\n    LIMIT ?`,\n    maxLoc, limit,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.file))\n    .map((r) => ({\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      file: r.file,\n      startLine: r.start_line,\n      endLine: r.end_line,\n      loc: r.loc,\n      singleCaller: r.caller_symbol,\n      singleCallerShort: shortenSymbol(r.caller_symbol),\n      callerFanIn: r.caller_fan_in,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport { getCalleeRowsForSymbol, testFileExclusionSql } from '../query-support.js';\nimport type { PassthroughCandidate } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find passthrough candidates: functions that just forward to one\n * other function.\n *\n * A function with exactly 1 callee and small LOC is likely a thin\n * wrapper that adds no value — it just passes arguments through to\n * the real implementation.\n */\nexport function passthroughCandidates(\n  db: ScipDatabase,\n  opts?: { scope?: string; maxLoc?: number; limit?: number },\n): PassthroughCandidate[] {\n  const { scope, maxLoc = 15, limit = 30 } = opts ?? {};\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  // 1. Find all non-trivial symbols with definition ranges (>= 3 LOC)\n  const symbols = db.all<{\n    id: number;\n    symbol: string;\n    document_id: number;\n    start_line: number;\n    end_line: number;\n    loc: number;\n    relative_path: string;\n  }>(\n    `SELECT\n      gs.id,\n      gs.symbol,\n      der.document_id,\n      der.start_line,\n      der.end_line,\n      (der.end_line - der.start_line + 1) AS loc,\n      d.relative_path\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      AND ${testFileExclusionSql('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND (der.end_line - der.start_line + 1) >= 3\n      AND (der.end_line - der.start_line + 1) <= ?\n      ${scopeFilter}\n    ORDER BY d.relative_path`,\n    maxLoc,\n  );\n\n  const results: PassthroughCandidate[] = [];\n\n  for (const sym of symbols) {\n    if (db.isIgnored(sym.relative_path)) continue;\n\n    // 2. Count callees for this symbol\n    const callees = getCalleeRowsForSymbol(db, {\n      documentId: sym.document_id,\n      startLine: sym.start_line,\n      endLine: sym.end_line,\n      symbolId: sym.id,\n    });\n\n    // Deduplicate by symbol (same callee may appear in multiple chunks)\n    const uniqueCallees = new Map<string, { symbol: string; file: string }>();\n    for (const c of callees) {\n      if (!uniqueCallees.has(c.symbol)) {\n        uniqueCallees.set(c.symbol, { symbol: c.symbol, file: c.file });\n      }\n    }\n\n    // 3. Passthrough = exactly 1 unique callee\n    if (uniqueCallees.size !== 1) continue;\n\n    const [, callee] = [...uniqueCallees.entries()][0]!;\n\n    results.push({\n      symbol: sym.symbol,\n      shortName: shortenSymbol(sym.symbol),\n      file: sym.relative_path,\n      startLine: sym.start_line,\n      endLine: sym.end_line,\n      loc: sym.loc,\n      forwardsTo: callee.symbol,\n      forwardsToShort: shortenSymbol(callee.symbol),\n      forwardsToFile: callee.file,\n    });\n  }\n\n  results.sort((a, b) => a.loc - b.loc || a.file.localeCompare(b.file));\n  return results.slice(0, limit);\n}\n","import type { ScipDatabase } from '../db.js';\nimport { testFileExclusionSql } from '../query-support.js';\nimport type { StaleAbstraction } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find stale abstractions: type-level symbols (classes, interfaces, type\n * aliases) that have 0 or 1 cross-file consumers.\n *\n * A type that only one file uses is over-abstracted — it was designed\n * for reuse that never materialized. Large single-consumer types are\n * the strongest signal of wasted abstraction.\n */\nexport function staleAbstractions(\n  db: ScipDatabase,\n  opts?: { scope?: string; minLoc?: number; limit?: number },\n): StaleAbstraction[] {\n  const { scope, minLoc = 3, limit = 30 } = opts ?? {};\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  const rows = db.all<{\n    symbol: string;\n    file: string;\n    start_line: number;\n    end_line: number;\n    loc: number;\n    consumers: number;\n  }>(\n    `SELECT * FROM (\n      SELECT\n        gs.symbol,\n        d.relative_path AS file,\n        der.start_line,\n        der.end_line,\n        (der.end_line - der.start_line + 1) AS loc,\n        (SELECT COUNT(DISTINCT ref_c.document_id)\n         FROM mentions ref_m\n         JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n         WHERE ref_m.symbol_id = gs.id\n           AND ref_m.role = 0\n           AND ref_c.document_id != der.document_id\n        ) AS consumers\n      FROM global_symbols gs\n      JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n      JOIN documents d ON der.document_id = d.id\n      WHERE 1 = 1\n        ${db.pathExclusionsFor('d')}\n        AND ${testFileExclusionSql('d')}\n        ${db.symbolNoiseFor('gs')}\n        -- Top-level type symbols: ends with # but does not contain nested #\n        AND gs.symbol LIKE '%#'\n        AND gs.symbol NOT LIKE '%#%#%'\n        AND (der.end_line - der.start_line + 1) >= ?\n        ${scopeFilter}\n    ) WHERE consumers <= 1\n    ORDER BY loc DESC\n    LIMIT ?`,\n    minLoc, limit,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.file))\n    // Exclude types defined in dedicated type files (types.ts, types/, etc.)\n    // These are intentional public API types, not premature abstractions.\n    .filter((r) => {\n      const basename = r.file.split('/').pop() ?? '';\n      const isTypeFile = basename.includes('types') || r.file.includes('/types/');\n      // Types in type files with 1 consumer are normal API types — skip them.\n      // Types in type files with 0 consumers are genuinely unused — keep them.\n      if (isTypeFile && r.consumers > 0) return false;\n      return true;\n    })\n    .map((r) => ({\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      file: r.file,\n      startLine: r.start_line,\n      endLine: r.end_line,\n      loc: r.loc,\n      consumers: r.consumers,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport { testFileExclusionSql } from '../query-support.js';\nimport type { ComplexityHotspot } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find complexity hotspots: symbols with a composite score based on\n * LOC, fan-in, fan-out, and callee count.\n *\n * Score = (loc / 50) * (fanIn / 5) * max(fanOut / 5, 1)\n *\n * High scores indicate symbols that are large, widely depended upon,\n * AND reach out to many other modules — the riskiest code to change.\n */\nexport function complexityHotspots(\n  db: ScipDatabase,\n  opts?: { scope?: string; minLoc?: number; limit?: number },\n): ComplexityHotspot[] {\n  const { scope, minLoc = 10, limit = 30 } = opts ?? {};\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  const rows = db.all<{\n    symbol: string;\n    file: string;\n    start_line: number;\n    end_line: number;\n    loc: number;\n    fan_in: number;\n    fan_out: number;\n    callee_count: number;\n  }>(\n    `SELECT\n      gs.symbol,\n      d.relative_path AS file,\n      der.start_line,\n      der.end_line,\n      (der.end_line - der.start_line + 1) AS loc,\n      -- fanIn: distinct files that reference this symbol\n      (SELECT COUNT(DISTINCT ref_c.document_id)\n       FROM mentions ref_m\n       JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n       WHERE ref_m.symbol_id = gs.id AND ref_m.role = 0\n      ) AS fan_in,\n      -- fanOut: distinct symbols referenced within this definition range\n      -- that are defined in different files\n      (SELECT COUNT(DISTINCT out_gs.id)\n       FROM mentions out_m\n       JOIN chunks out_c ON out_m.chunk_id = out_c.id\n       JOIN global_symbols out_gs ON out_m.symbol_id = out_gs.id\n       JOIN defn_enclosing_ranges out_der ON out_gs.id = out_der.symbol_id\n       WHERE out_c.document_id = der.document_id\n         AND out_c.start_line >= der.start_line\n         AND out_c.end_line <= der.end_line\n         AND out_m.role = 0\n         AND out_gs.id != gs.id\n         AND out_der.document_id != der.document_id\n      ) AS fan_out,\n      -- calleeCount: total distinct callees within definition range\n      (SELECT COUNT(DISTINCT callee_gs.id)\n       FROM mentions callee_m\n       JOIN chunks callee_c ON callee_m.chunk_id = callee_c.id\n       JOIN global_symbols callee_gs ON callee_m.symbol_id = callee_gs.id\n       WHERE callee_c.document_id = der.document_id\n         AND callee_c.start_line >= der.start_line\n         AND callee_c.end_line <= der.end_line\n         AND callee_m.role = 0\n         AND callee_gs.id != gs.id\n      ) AS callee_count\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE 1 = 1\n      ${db.pathExclusionsFor('d')}\n      AND ${testFileExclusionSql('d')}\n      ${db.symbolNoiseFor('gs')}\n      AND (der.end_line - der.start_line + 1) >= ?\n      ${scopeFilter}\n    ORDER BY (\n      CAST((der.end_line - der.start_line + 1) AS REAL) / 50.0\n      * CAST((SELECT COUNT(DISTINCT ref_c2.document_id)\n              FROM mentions ref_m2\n              JOIN chunks ref_c2 ON ref_m2.chunk_id = ref_c2.id\n              WHERE ref_m2.symbol_id = gs.id AND ref_m2.role = 0\n             ) AS REAL) / 5.0\n      * MAX(CAST((SELECT COUNT(DISTINCT out_gs2.id)\n                  FROM mentions out_m2\n                  JOIN chunks out_c2 ON out_m2.chunk_id = out_c2.id\n                  JOIN global_symbols out_gs2 ON out_m2.symbol_id = out_gs2.id\n                  JOIN defn_enclosing_ranges out_der2 ON out_gs2.id = out_der2.symbol_id\n                  WHERE out_c2.document_id = der.document_id\n                    AND out_c2.start_line >= der.start_line\n                    AND out_c2.end_line <= der.end_line\n                    AND out_m2.role = 0\n                    AND out_gs2.id != gs.id\n                    AND out_der2.document_id != der.document_id\n                 ) AS REAL) / 5.0, 1.0)\n    ) DESC\n    LIMIT ?`,\n    minLoc, limit,\n  );\n\n  return rows\n    .filter((r) => !db.isIgnored(r.file))\n    .map((r) => ({\n      symbol: r.symbol,\n      shortName: shortenSymbol(r.symbol),\n      file: r.file,\n      startLine: r.start_line,\n      endLine: r.end_line,\n      loc: r.loc,\n      fanIn: r.fan_in,\n      fanOut: r.fan_out,\n      calleeCount: r.callee_count,\n      score:\n        Math.round(\n          (r.loc / 50) * (r.fan_in / 5) * Math.max(r.fan_out / 5, 1) * 100,\n        ) / 100,\n    }));\n}\n","import type { ScipDatabase } from '../db.js';\nimport { dead } from './dead.js';\nimport { isolated } from './isolated.js';\nimport { cycles } from './cycles.js';\nimport { similarAll } from './similar.js';\nimport { extractCandidates } from './extract-candidates.js';\nimport { wrapperCandidates } from './wrapper-candidates.js';\nimport { passthroughCandidates } from './passthrough-candidates.js';\nimport { staleAbstractions } from './stale-abstractions.js';\nimport { drift } from './drift.js';\nimport { complexityHotspots } from './complexity-hotspots.js';\nimport { testCoverageSummary } from './test-coverage.js';\nimport { stats } from './stats.js';\nimport type { HealthAction, HealthReport } from '../types.js';\n\n/**\n * Single composite health report that runs all de-bloat analyses\n * and produces a prioritized action list.\n *\n * The scoring formula accounts for common false positives:\n * - Entry points (CLI, workers, barrels) appearing as \"dead code\"\n * - Typed result interfaces with 1 consumer (normal for APIs)\n * - Consistent import patterns across sibling modules (not duplication)\n * - Barrel and orchestrator files deviating from sibling patterns (expected)\n */\nexport function health(\n  db: ScipDatabase,\n  opts: { scope?: string } = {},\n): HealthReport {\n  const { scope } = opts;\n\n  // Run all analyses\n  const s = stats(db);\n  const deadResult = dead(db, { scope, minLoc: 3, skipBarrels: false });\n  const isolatedResult = isolated(db, { scope, minLoc: 3 });\n  const cycleResult = cycles(db, { scope });\n  const similarResult = similarAll(db, { scope, minSimilarity: 0.6, limit: 50, minCallees: 4 });\n  const extractResult = extractCandidates(db, { scope, minLoc: 15, minCallees: 5, limit: 50 });\n  const wrapperResult = wrapperCandidates(db, { scope, maxLoc: 15, limit: 50 });\n  const passthroughResult = passthroughCandidates(db, { scope, maxLoc: 15, limit: 50 });\n  const staleResult = staleAbstractions(db, { scope, minLoc: 3, limit: 50 });\n  const driftResult = drift(db, { scope });\n  const complexResult = complexityHotspots(db, { scope, minLoc: 10, limit: 10 });\n  const testResult = testCoverageSummary(db, { scope, minLoc: 3 });\n\n  const isolatedLoc = isolatedResult.reduce((sum, r) => sum + r.loc, 0);\n\n  // ── False-positive filtering ─────────────────────────────\n\n  // Entry points and barrels appear as dead/isolated because nothing imports them.\n  // Filter them out of the scoring (but still report them with a note).\n  const entryPointPatterns = ['/index.ts', '/index.js', 'cli.ts', 'worker.ts', 'postinstall.ts', '/mod.rs', '__init__.py', 'main.ts', 'main.rs', 'main.go', 'main.py'];\n  const isEntryPoint = (path: string) => entryPointPatterns.some((p) => path.endsWith(p));\n\n  // Dead code: only count truly dead symbols (zero refs anywhere),\n  // excluding entry points AND file-internal helpers (which are fine).\n  const trueDeadSymbols = deadResult.symbols.filter(\n    (s) => !isEntryPoint(s.relativePath) && s.kind === 'dead-code',\n  );\n  const trueDeadCount = trueDeadSymbols.length;\n  const trueDeadLoc = trueDeadSymbols.reduce((sum, s) => sum + s.loc, 0);\n  const fileInternalCount = deadResult.symbols.filter(\n    (s) => !isEntryPoint(s.relativePath) && s.kind === 'file-internal',\n  ).length;\n\n  // Isolated: same entry-point filtering\n  const trueIsolatedCount = isolatedResult.filter(\n    (s) => !isEntryPoint(s.relativePath),\n  ).length;\n\n  // Stale abstractions: the command filters out types.ts single-consumer types.\n  // Also filter out 0-consumer types in files that export functions — these are\n  // likely parameter/return types consumed through function signatures, which\n  // the SCIP index can't track as direct mentions.\n  const filesWithFunctions = new Set(\n    db.all<{ relative_path: string }>(\n      `SELECT DISTINCT d.relative_path\n       FROM global_symbols gs\n       JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n       JOIN documents d ON der.document_id = d.id\n       WHERE gs.symbol LIKE '%().'\n         ${db.pathExclusionsFor('d')}`,\n    ).map((r) => r.relative_path),\n  );\n  const trueStaleCount = staleResult.filter((s) => {\n    // 0-consumer types in files with functions are likely param/return types\n    if (s.consumers === 0 && filesWithFunctions.has(s.file)) return false;\n    return true;\n  }).length;\n\n  // Drift: now uses usage-based detection (unused imports, layer violations, pattern deviations)\n  // The drift command already filters structural roles internally.\n  const trueDriftCount = driftResult.results.length;\n\n  // Similar pairs: the similar command now uses TF-IDF weighted cosine\n  // similarity which automatically discounts infrastructure callees.\n  // The sharedCallees list only contains significant (above-median IDF) callees.\n  // We can trust the count directly.\n  const trueSimilarCount = similarResult.length;\n\n  // ── Build prioritized action list ────────────────────────\n\n  const actions: HealthAction[] = [];\n\n  if (trueDeadCount > 0) {\n    actions.push({\n      category: 'Dead code',\n      description: `${trueDeadCount} symbols with zero references anywhere — safe to delete`,\n      effort: 'low',\n      impact: 'high',\n      count: trueDeadCount,\n      locRecoverable: trueDeadLoc,\n    });\n  }\n\n  if (testResult.percent < 50) {\n    actions.push({\n      category: 'Test coverage',\n      description: `${testResult.percent}% of symbols referenced by tests (${testResult.uncovered} uncovered)`,\n      effort: 'high',\n      impact: 'high',\n      count: testResult.uncovered,\n      locRecoverable: 0,\n    });\n  }\n\n  if (trueIsolatedCount > 0) {\n    actions.push({\n      category: 'Isolated symbols',\n      description: `${trueIsolatedCount} symbols completely disconnected from the codebase graph`,\n      effort: 'low',\n      impact: 'medium',\n      count: trueIsolatedCount,\n      locRecoverable: isolatedResult\n        .filter((s) => !isEntryPoint(s.relativePath))\n        .reduce((sum, s) => sum + s.loc, 0),\n    });\n  }\n\n  if (cycleResult.length > 0) {\n    actions.push({\n      category: 'Circular dependencies',\n      description: `${cycleResult.length} cycle(s) — break with dependency inversion or module restructuring`,\n      effort: 'medium',\n      impact: 'high',\n      count: cycleResult.length,\n      locRecoverable: 0,\n    });\n  }\n\n  if (trueSimilarCount > 0) {\n    actions.push({\n      category: 'Similar functions',\n      description: `${trueSimilarCount} pairs with real logic overlap (beyond shared imports) — consolidation candidates`,\n      effort: 'medium',\n      impact: 'medium',\n      count: trueSimilarCount,\n      locRecoverable: 0,\n    });\n  }\n\n  if (extractResult.length > 0) {\n    actions.push({\n      category: 'Extraction candidates',\n      description: `${extractResult.length} large functions with isolated callee clusters — extract method opportunities`,\n      effort: 'medium',\n      impact: 'medium',\n      count: extractResult.length,\n      locRecoverable: 0,\n    });\n  }\n\n  if (wrapperResult.length > 0) {\n    actions.push({\n      category: 'Wrapper functions',\n      description: `${wrapperResult.length} single-consumer symbols that could be inlined`,\n      effort: 'low',\n      impact: 'low',\n      count: wrapperResult.length,\n      locRecoverable: wrapperResult.reduce((sum, r) => sum + r.loc, 0),\n    });\n  }\n\n  if (passthroughResult.length > 0) {\n    actions.push({\n      category: 'Passthrough functions',\n      description: `${passthroughResult.length} functions that just forward to one callee — unnecessary indirection`,\n      effort: 'low',\n      impact: 'low',\n      count: passthroughResult.length,\n      locRecoverable: passthroughResult.reduce((sum, r) => sum + r.loc, 0),\n    });\n  }\n\n  if (trueStaleCount > 0) {\n    // Count from the filtered set, not the raw result\n    const trueStaleSymbols = staleResult.filter((s) => {\n      if (s.consumers === 0 && filesWithFunctions.has(s.file)) return false;\n      return true;\n    });\n    const unused = trueStaleSymbols.filter((s) => s.consumers === 0).length;\n    const singleUse = trueStaleCount - unused;\n    const parts: string[] = [];\n    if (unused > 0) parts.push(`${unused} unused`);\n    if (singleUse > 0) parts.push(`${singleUse} single-consumer (not in types file)`);\n    actions.push({\n      category: 'Stale abstractions',\n      description: `${parts.join(', ')} — premature abstraction`,\n      effort: 'low',\n      impact: 'medium',\n      count: trueStaleCount,\n      locRecoverable: staleResult\n        .filter((s) => s.consumers === 0 || !s.file.includes('types'))\n        .reduce((sum, r) => sum + r.loc, 0),\n    });\n  }\n\n  if (trueDriftCount > 0) {\n    const parts: string[] = [];\n    if (driftResult.unusedImports > 0) parts.push(`${driftResult.unusedImports} unused imports`);\n    if (driftResult.layerViolations > 0) parts.push(`${driftResult.layerViolations} layer violations`);\n    if (driftResult.patternDeviations > 0) parts.push(`${driftResult.patternDeviations} unique deps`);\n    actions.push({\n      category: 'Structural drift',\n      description: parts.join(', '),\n      effort: driftResult.layerViolations > 0 ? 'medium' : 'low',\n      impact: driftResult.layerViolations > 0 ? 'medium' : 'low',\n      count: trueDriftCount,\n      locRecoverable: 0,\n    });\n  }\n\n  // Sort: high impact + low effort first\n  const impactWeight = { high: 3, medium: 2, low: 1 };\n  const effortWeight = { low: 3, medium: 2, high: 1 };\n  actions.sort((a, b) => {\n    const scoreA = impactWeight[a.impact] * effortWeight[a.effort];\n    const scoreB = impactWeight[b.impact] * effortWeight[b.effort];\n    return scoreB - scoreA;\n  });\n\n  // ── Compute health score (0-100) ─────────────────────────\n  //\n  // Uses filtered counts (false positives removed).\n  // Deductions scale with codebase size so a 10-file project\n  // and a 1000-file project aren't penalized the same way.\n  const fileCount = Math.max(s.documents, 1);\n  const symbolCount = Math.max(s.symbols, 1);\n\n  let score = 100;\n\n  // Dead code: deduct based on % of symbols that are dead, not raw count\n  const deadPercent = trueDeadCount / symbolCount;\n  score -= Math.min(20, Math.round(deadPercent * 200));\n\n  // Isolated: same percentage-based\n  const isolatedPercent = trueIsolatedCount / symbolCount;\n  score -= Math.min(10, Math.round(isolatedPercent * 200));\n\n  // Cycles: these are always bad, flat penalty\n  score -= Math.min(15, cycleResult.length * 5);\n\n  // Similar pairs: only count true logic overlap, not boilerplate\n  score -= Math.min(10, trueSimilarCount * 2);\n\n  // Extract candidates: mild penalty\n  score -= Math.min(5, extractResult.length * 2);\n\n  // Wrappers: mild\n  score -= Math.min(3, wrapperResult.length);\n\n  // Passthroughs: mild\n  score -= Math.min(3, passthroughResult.length);\n\n  // Stale abstractions: percentage-based with filtered count\n  const stalePercent = trueStaleCount / Math.max(symbolCount * 0.1, 1);\n  score -= Math.min(8, Math.round(stalePercent * 10));\n\n  // Drift: percentage of files that deviate\n  const driftPercent = trueDriftCount / fileCount;\n  score -= Math.min(5, Math.round(driftPercent * 50));\n\n  // Complexity: only penalize extreme outliers\n  const extremeComplexity = complexResult.filter((r) => r.score > 50).length;\n  score -= Math.min(5, extremeComplexity * 2);\n\n  // Test coverage: significant penalty for low coverage\n  // 0% = -15, 25% = -11, 50% = -7, 75% = -4, 100% = 0\n  const coverageDeduction = Math.round(15 * (1 - testResult.percent / 100));\n  score -= coverageDeduction;\n\n  score = Math.max(0, Math.min(100, score));\n\n  return {\n    score,\n    overview: {\n      documents: s.documents,\n      symbols: s.symbols,\n      indexSizeBytes: s.indexSizeBytes,\n    },\n    findings: {\n      deadSymbols: trueDeadCount,\n      deadLoc: trueDeadLoc,\n      isolatedSymbols: trueIsolatedCount,\n      isolatedLoc: isolatedResult\n        .filter((s) => !isEntryPoint(s.relativePath))\n        .reduce((sum, s) => sum + s.loc, 0),\n      cycles: cycleResult.length,\n      similarPairs: trueSimilarCount,\n      extractionCandidates: extractResult.length,\n      wrappers: wrapperResult.length,\n      passthroughs: passthroughResult.length,\n      staleTypes: trueStaleCount,\n      driftedFiles: trueDriftCount,\n      complexityHotspotCount: complexResult.length,\n      testCoveragePercent: testResult.percent,\n    },\n    actions,\n    topComplexity: complexResult.slice(0, 5).map((r) => ({\n      symbol: r.shortName,\n      score: r.score,\n    })),\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport { findFirstSymbolMatch, getCalleeRowsForSymbol } from '../query-support.js';\nimport type { ConvergenceResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Given two similar symbols, show what a consolidated version would look like.\n * The shared callee set becomes the common body. The unique callees become\n * the parameterization points.\n */\nexport function convergence(\n  db: ScipDatabase,\n  symbolPatternA: string,\n  symbolPatternB: string,\n): ConvergenceResult | null {\n  const matchA = findFirstSymbolMatch(db, symbolPatternA);\n  const matchB = findFirstSymbolMatch(db, symbolPatternB);\n\n  if (!matchA || !matchB) return null;\n\n  const calleesA = new Set(\n    getCalleeRowsForSymbol(db, matchA).map((r) => r.symbol),\n  );\n  const calleesB = new Set(\n    getCalleeRowsForSymbol(db, matchB).map((r) => r.symbol),\n  );\n\n  const shared: string[] = [];\n  for (const c of calleesA) {\n    if (calleesB.has(c)) shared.push(c);\n  }\n\n  const uniqueA: string[] = [];\n  for (const c of calleesA) {\n    if (!calleesB.has(c)) uniqueA.push(c);\n  }\n\n  const uniqueB: string[] = [];\n  for (const c of calleesB) {\n    if (!calleesA.has(c)) uniqueB.push(c);\n  }\n\n  const union = new Set([...calleesA, ...calleesB]);\n  const similarity = union.size > 0 ? shared.length / union.size : 0;\n\n  // Generate a consolidation strategy description\n  let strategy: string;\n  if (uniqueA.length === 0 && uniqueB.length === 0) {\n    strategy = 'These functions have identical callee sets. One can replace the other directly.';\n  } else if (uniqueA.length === 0) {\n    strategy = `A is a subset of B. A can be replaced by calling B (B does everything A does plus more).`;\n  } else if (uniqueB.length === 0) {\n    strategy = `B is a subset of A. B can be replaced by calling A (A does everything B does plus more).`;\n  } else if (uniqueA.length <= 2 && uniqueB.length <= 2) {\n    strategy = `Create a shared function with the ${shared.length} common callees. Pass the ${uniqueA.length + uniqueB.length} divergent callees as parameters or strategy callbacks.`;\n  } else {\n    strategy = `Extract the ${shared.length} shared callees into a common helper. Each function calls the helper plus its own unique logic (${uniqueA.length} callees in A, ${uniqueB.length} in B).`;\n  }\n\n  const locA = matchA.endLine - matchA.startLine + 1;\n  const locB = matchB.endLine - matchB.startLine + 1;\n\n  return {\n    symbolA: {\n      symbol: matchA.symbol,\n      shortName: shortenSymbol(matchA.symbol),\n      file: matchA.relativePath,\n      loc: locA,\n    },\n    symbolB: {\n      symbol: matchB.symbol,\n      shortName: shortenSymbol(matchB.symbol),\n      file: matchB.relativePath,\n      loc: locB,\n    },\n    similarity,\n    sharedCallees: shared.map(shortenSymbol),\n    uniqueToA: uniqueA.map(shortenSymbol),\n    uniqueToB: uniqueB.map(shortenSymbol),\n    consolidationStrategy: strategy,\n  };\n}\n","import { readFileSync } from 'node:fs';\nimport { join } from 'node:path';\nimport type { ScipDatabase } from '../db.js';\nimport { findFirstSymbolMatch } from '../query-support.js';\nimport type { CodeResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Read the source code for a symbol, bounded to its definition range.\n * Language-agnostic: just reads the file and extracts the relevant lines.\n *\n * Accepts:\n *   - Symbol name pattern: \"processVegaMention\"\n *   - Full short name: \"src:modules:chat:processVegaMention\"\n *   - File:line-line syntax: \"src/chat/service.ts:100-200\"\n */\nexport function code(\n  db: ScipDatabase,\n  symbolPattern: string,\n  opts: { context?: number } = {},\n): CodeResult | null {\n  const { context = 0 } = opts;\n\n  // Handle direct file:line-line syntax (bypass symbol lookup)\n  const fileLineMatch = symbolPattern.match(/^(.+\\.\\w+):(\\d+)-(\\d+)$/);\n  if (fileLineMatch) {\n    return readFileRange(db, fileLineMatch[1]!, parseInt(fileLineMatch[2]!, 10), parseInt(fileLineMatch[3]!, 10), context);\n  }\n\n  const match = findFirstSymbolMatch(db, symbolPattern);\n  if (!match) return null;\n\n  // Get the language from the documents table\n  const doc = db.get<{ language: string | null }>(\n    `SELECT language FROM documents WHERE relative_path = ?`,\n    match.relativePath,\n  );\n\n  // Read the file\n  const filePath = join(db.config.projectRoot, match.relativePath);\n  let fileContent: string;\n  try {\n    fileContent = readFileSync(filePath, 'utf-8');\n  } catch {\n    return null;\n  }\n\n  const lines = fileContent.split('\\n');\n  const startLine = Math.max(0, match.startLine - context);\n  const endLine = Math.min(lines.length - 1, match.endLine + context);\n  const source = lines.slice(startLine, endLine + 1).join('\\n');\n\n  return {\n    symbol: match.symbol,\n    shortName: shortenSymbol(match.symbol),\n    relativePath: match.relativePath,\n    startLine: startLine + 1, // 1-indexed for display\n    endLine: endLine + 1,\n    language: doc?.language ?? null,\n    source,\n  };\n}\n\n/** Read source by file path and line range directly (no symbol lookup) */\nfunction readFileRange(\n  db: ScipDatabase,\n  filePath: string,\n  startLine: number,\n  endLine: number,\n  context: number,\n): CodeResult | null {\n  // Find the file in the index\n  const doc = db.get<{ relative_path: string; language: string | null }>(\n    `SELECT relative_path, language FROM documents WHERE relative_path LIKE ?`,\n    `%${filePath}%`,\n  );\n  if (!doc) return null;\n\n  const fullPath = join(db.config.projectRoot, doc.relative_path);\n  let fileContent: string;\n  try {\n    fileContent = readFileSync(fullPath, 'utf-8');\n  } catch {\n    return null;\n  }\n\n  const lines = fileContent.split('\\n');\n  const start = Math.max(0, startLine - 1 - context); // convert to 0-indexed\n  const end = Math.min(lines.length - 1, endLine - 1 + context);\n  const source = lines.slice(start, end + 1).join('\\n');\n\n  return {\n    symbol: `${doc.relative_path}:${startLine}-${endLine}`,\n    shortName: `${doc.relative_path}:${startLine}-${endLine}`,\n    relativePath: doc.relative_path,\n    startLine: start + 1,\n    endLine: end + 1,\n    language: doc.language,\n    source,\n  };\n}\n","import { readFileSync } from 'node:fs';\nimport { join } from 'node:path';\nimport type { ScipDatabase } from '../db.js';\nimport { findFirstSymbolMatch, getCalleeRowsForSymbol } from '../query-support.js';\nimport type { ComplexityResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Per-symbol complexity analysis combining source-level branch counting\n * with index-level metrics (fan-in, fan-out, callee count).\n *\n * Branch counting uses language-aware regex. The language is read from\n * the SCIP documents table, so it works for any indexed language.\n */\nexport function complexity(\n  db: ScipDatabase,\n  symbolPattern: string,\n): ComplexityResult | null {\n  const match = findFirstSymbolMatch(db, symbolPattern);\n  if (!match) return null;\n\n  // Get language\n  const doc = db.get<{ language: string | null }>(\n    `SELECT language FROM documents WHERE relative_path = ?`,\n    match.relativePath,\n  );\n  const language = doc?.language ?? 'unknown';\n\n  // Read source for branch counting\n  const filePath = join(db.config.projectRoot, match.relativePath);\n  let source = '';\n  try {\n    const lines = readFileSync(filePath, 'utf-8').split('\\n');\n    source = lines.slice(match.startLine, match.endLine + 1).join('\\n');\n  } catch {\n    // If we can't read the file, just skip branch counting\n  }\n\n  const branches = countBranches(source, language);\n  const loc = match.endLine - match.startLine + 1;\n\n  // Callee count\n  const callees = getCalleeRowsForSymbol(db, match);\n  const uniqueCallees = new Set(callees.map((c) => c.symbol));\n\n  // Fan-in\n  const fanInRow = db.get<{ c: number }>(\n    `SELECT COUNT(DISTINCT c.document_id) AS c\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    WHERE m.symbol_id = ? AND m.role = 0`,\n    match.symbolId,\n  );\n\n  // Fan-out (callees in other files)\n  const fanOut = new Set(\n    callees.filter((c) => c.file !== match.relativePath).map((c) => c.symbol),\n  ).size;\n\n  return {\n    symbol: match.symbol,\n    shortName: shortenSymbol(match.symbol),\n    relativePath: match.relativePath,\n    startLine: match.startLine,\n    endLine: match.endLine,\n    loc,\n    branches,\n    cyclomaticEstimate: branches + 1,\n    calleeCount: uniqueCallees.size,\n    fanIn: fanInRow?.c ?? 0,\n    fanOut,\n  };\n}\n\n/**\n * Count branch points in source code using language-aware regex.\n * Works across all SCIP-supported languages.\n */\nfunction countBranches(source: string, language: string): number {\n  // Strip comments and strings to avoid false positives\n  const stripped = stripCommentsAndStrings(source);\n  let count = 0;\n\n  // Universal branch keywords (work across most C-family languages)\n  const universalPatterns = [\n    /\\bif\\b/g,\n    /\\belse\\s+if\\b/g,\n    /\\belse\\b/g,\n    /\\bfor\\b/g,\n    /\\bwhile\\b/g,\n    /\\bswitch\\b/g,\n    /\\bcase\\b/g,\n    /\\bcatch\\b/g,\n    /\\?\\s*[^?]/g,    // ternary (but not ??)\n    /&&/g,\n    /\\|\\|/g,\n  ];\n\n  for (const pattern of universalPatterns) {\n    const matches = stripped.match(pattern);\n    if (matches) count += matches.length;\n  }\n\n  // Language-specific patterns\n  if (language === 'python') {\n    const pyPatterns = [/\\belif\\b/g, /\\bexcept\\b/g, /\\bfinally\\b/g];\n    for (const p of pyPatterns) {\n      const m = stripped.match(p);\n      if (m) count += m.length;\n    }\n  } else if (language === 'rust') {\n    const rustPatterns = [/\\bmatch\\b/g, /=>/g, /\\bloop\\b/g];\n    for (const p of rustPatterns) {\n      const m = stripped.match(p);\n      if (m) count += m.length;\n    }\n  } else if (language === 'ruby') {\n    const rubyPatterns = [/\\belsif\\b/g, /\\bunless\\b/g, /\\brescue\\b/g, /\\bwhen\\b/g];\n    for (const p of rubyPatterns) {\n      const m = stripped.match(p);\n      if (m) count += m.length;\n    }\n  } else if (language === 'go') {\n    const goPatterns = [/\\bselect\\b/g, /\\bdefer\\b/g];\n    for (const p of goPatterns) {\n      const m = stripped.match(p);\n      if (m) count += m.length;\n    }\n  }\n\n  return count;\n}\n\n/**\n * Rough strip of comments and string literals to reduce false positives\n * in branch counting. Not perfect but good enough for estimation.\n */\nfunction stripCommentsAndStrings(source: string): string {\n  return source\n    // Block comments\n    .replace(/\\/\\*[\\s\\S]*?\\*\\//g, '')\n    // Line comments\n    .replace(/\\/\\/.*/g, '')\n    // Python/Ruby line comments\n    .replace(/#.*/g, '')\n    // Double-quoted strings\n    .replace(/\"(?:[^\"\\\\]|\\\\.)*\"/g, '\"\"')\n    // Single-quoted strings\n    .replace(/'(?:[^'\\\\]|\\\\.)*'/g, \"''\")\n    // Template literals\n    .replace(/`(?:[^`\\\\]|\\\\.)*`/g, '``');\n}\n","import type { ScipDatabase } from '../db.js';\nimport { findFirstSymbolMatch } from '../query-support.js';\nimport type { DataflowResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Reference-level dataflow analysis: where does data around this symbol\n * come from and where does it go?\n *\n * This is not value-level dataflow (we can't trace x = foo(); bar(x);\n * as a chain). Instead it shows:\n * - Where the symbol is defined and used\n * - What other symbols appear in the same enclosing scope (co-occurring data)\n * - What feeds into the function that defines it (producers)\n * - What consumes the function that uses it (consumers)\n *\n * Language-agnostic: works with any SCIP index.\n */\nexport function dataflow(\n  db: ScipDatabase,\n  symbolPattern: string,\n): DataflowResult | null {\n  const match = findFirstSymbolMatch(db, symbolPattern);\n  if (!match) return null;\n\n  // Definition sites (role=1)\n  const defSites = db.all<{ file: string; line: number }>(\n    `SELECT d.relative_path AS file, c.start_line AS line\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d ON c.document_id = d.id\n    WHERE m.symbol_id = ? AND m.role = 1\n    ORDER BY d.relative_path, c.start_line`,\n    match.symbolId,\n  );\n\n  // Usage sites (role=0) with enclosing symbol\n  const usageSites = db.all<{\n    file: string;\n    line: number;\n    enclosing_symbol: string | null;\n  }>(\n    `SELECT d.relative_path AS file, c.start_line AS line,\n      (SELECT enc_gs.symbol\n       FROM defn_enclosing_ranges enc_der\n       JOIN global_symbols enc_gs ON enc_der.symbol_id = enc_gs.id\n       WHERE enc_der.document_id = d.id\n         AND enc_der.start_line <= c.start_line\n         AND enc_der.end_line >= c.end_line\n       ORDER BY (enc_der.end_line - enc_der.start_line) ASC\n       LIMIT 1\n      ) AS enclosing_symbol\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents d ON c.document_id = d.id\n    WHERE m.symbol_id = ? AND m.role = 0\n      ${db.pathExclusionsFor('d')}\n    ORDER BY d.relative_path, c.start_line`,\n    match.symbolId,\n  );\n\n  // Producers: other symbols referenced within the same function that defines our target\n  const producers = db.all<{ symbol: string; file: string }>(\n    `SELECT DISTINCT other_gs.symbol, other_d.relative_path AS file\n    FROM mentions other_m\n    JOIN chunks other_c ON other_m.chunk_id = other_c.id\n    JOIN global_symbols other_gs ON other_m.symbol_id = other_gs.id\n    JOIN defn_enclosing_ranges other_der ON other_gs.id = other_der.symbol_id\n    JOIN documents other_d ON other_der.document_id = other_d.id\n    WHERE other_c.document_id = ?\n      AND other_c.start_line >= ? AND other_c.end_line <= ?\n      AND other_m.role = 0\n      AND other_gs.id != ?\n      ${db.symbolNoiseFor('other_gs')}\n      ${db.pathExclusionsFor('other_d')}\n    ORDER BY other_d.relative_path\n    LIMIT 30`,\n    match.documentId, match.startLine, match.endLine, match.symbolId,\n  );\n\n  // Consumers: symbols exported/defined by functions that reference our target\n  // (what does the data flow into after being used)\n  const consumers = db.all<{ symbol: string; file: string }>(\n    `SELECT DISTINCT consumer_gs.symbol, consumer_d.relative_path AS file\n    FROM mentions ref_m\n    JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n    JOIN documents ref_d ON ref_c.document_id = ref_d.id\n    -- Find the enclosing function at each usage site\n    JOIN defn_enclosing_ranges enc_der\n      ON enc_der.document_id = ref_d.id\n      AND enc_der.start_line <= ref_c.start_line\n      AND enc_der.end_line >= ref_c.end_line\n    JOIN global_symbols enc_gs ON enc_der.symbol_id = enc_gs.id\n    -- Find other symbols defined by that enclosing function's file\n    JOIN mentions consumer_m ON consumer_m.symbol_id = enc_gs.id AND consumer_m.role = 0\n    JOIN chunks consumer_c ON consumer_m.chunk_id = consumer_c.id\n    JOIN documents consumer_d ON consumer_c.document_id = consumer_d.id\n    JOIN global_symbols consumer_gs ON consumer_m.symbol_id = consumer_gs.id\n    WHERE ref_m.symbol_id = ? AND ref_m.role = 0\n      AND consumer_d.id != ref_d.id\n      ${db.symbolNoiseFor('consumer_gs')}\n      ${db.pathExclusionsFor('consumer_d')}\n    ORDER BY consumer_d.relative_path\n    LIMIT 30`,\n    match.symbolId,\n  );\n\n  return {\n    symbol: match.symbol,\n    shortName: shortenSymbol(match.symbol),\n    relativePath: match.relativePath,\n    definitionSites: defSites.filter((s) => !db.isIgnored(s.file)),\n    usageSites: usageSites\n      .filter((s) => !db.isIgnored(s.file))\n      .map((s) => ({\n        file: s.file,\n        line: s.line,\n        enclosingSymbol: s.enclosing_symbol ?? '(top-level)',\n        enclosingShort: s.enclosing_symbol ? shortenSymbol(s.enclosing_symbol) : '(top-level)',\n      })),\n    producers: producers\n      .filter((p) => !db.isIgnored(p.file))\n      .map((p) => ({ symbol: p.symbol, shortName: shortenSymbol(p.symbol), file: p.file })),\n    consumers: consumers\n      .filter((c) => !db.isIgnored(c.file))\n      .map((c) => ({ symbol: c.symbol, shortName: shortenSymbol(c.symbol), file: c.file })),\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport { findFirstSymbolMatch, getCalleeRowsForSymbol, type SymbolMatch } from '../query-support.js';\nimport type { SliceResult } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Reference-level program slicing: track what affects a symbol (backward)\n * or what a symbol affects (forward).\n *\n * Backward slice: \"What feeds into this?\" — symbols referenced in the same\n * function that defines the target. These are the inputs/dependencies.\n *\n * Forward slice: \"What does this feed into?\" — at each site where the target\n * is referenced, find the enclosing function, then find what that function\n * exports/defines. These are the outputs/consumers.\n *\n * Language-agnostic: works with any SCIP index.\n */\nexport function slice(\n  db: ScipDatabase,\n  symbolPattern: string,\n  opts: { direction?: 'backward' | 'forward' } = {},\n): SliceResult | null {\n  const { direction = 'backward' } = opts;\n\n  const match = findFirstSymbolMatch(db, symbolPattern);\n  if (!match) return null;\n\n  if (direction === 'backward') {\n    return backwardSlice(db, match);\n  } else {\n    return forwardSlice(db, match);\n  }\n}\n\n\nfunction backwardSlice(db: ScipDatabase, match: SymbolMatch): SliceResult {\n  // Find all symbols referenced within the definition range of the target.\n  // These are what \"feeds into\" the target — the inputs.\n  const callees = getCalleeRowsForSymbol(db, match);\n\n  // Also find symbols whose definitions are in the same file and whose\n  // ranges overlap or precede the target — local variables, parameters, etc.\n  const localPredecessors = db.all<{ symbol: string; file: string }>(\n    `SELECT DISTINCT gs.symbol, d.relative_path AS file\n    FROM defn_enclosing_ranges der\n    JOIN global_symbols gs ON der.symbol_id = gs.id\n    JOIN documents d ON der.document_id = d.id\n    WHERE der.document_id = ?\n      AND der.end_line < ?\n      AND gs.id != ?\n      ${db.symbolNoiseFor('gs')}\n    ORDER BY der.start_line DESC\n    LIMIT 15`,\n    match.documentId, match.startLine, match.symbolId,\n  );\n\n  const seen = new Set<string>();\n  const connected: SliceResult['connectedSymbols'] = [];\n\n  for (const c of callees) {\n    if (seen.has(c.symbol)) continue;\n    seen.add(c.symbol);\n    connected.push({\n      symbol: c.symbol,\n      shortName: shortenSymbol(c.symbol),\n      file: c.file,\n      relationship: 'referenced within definition (callee)',\n    });\n  }\n\n  for (const p of localPredecessors) {\n    if (seen.has(p.symbol) || db.isIgnored(p.file)) continue;\n    seen.add(p.symbol);\n    connected.push({\n      symbol: p.symbol,\n      shortName: shortenSymbol(p.symbol),\n      file: p.file,\n      relationship: 'defined before target in same file (local predecessor)',\n    });\n  }\n\n  return {\n    symbol: match.symbol,\n    shortName: shortenSymbol(match.symbol),\n    direction: 'backward',\n    connectedSymbols: connected,\n  };\n}\n\nfunction forwardSlice(db: ScipDatabase, match: SymbolMatch): SliceResult {\n  // Find where the target is referenced, then at each reference site,\n  // find what else the enclosing function defines/exports.\n  const rows = db.all<{\n    enclosing_symbol: string;\n    enclosing_file: string;\n    output_symbol: string;\n    output_file: string;\n  }>(\n    `SELECT DISTINCT\n      enc_gs.symbol AS enclosing_symbol,\n      enc_d.relative_path AS enclosing_file,\n      out_gs.symbol AS output_symbol,\n      out_d.relative_path AS output_file\n    FROM mentions ref_m\n    JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n    JOIN documents ref_d ON ref_c.document_id = ref_d.id\n    -- Find enclosing function at each reference site\n    JOIN defn_enclosing_ranges enc_der\n      ON enc_der.document_id = ref_d.id\n      AND enc_der.start_line <= ref_c.start_line\n      AND enc_der.end_line >= ref_c.end_line\n    JOIN global_symbols enc_gs ON enc_der.symbol_id = enc_gs.id\n    JOIN documents enc_d ON enc_der.document_id = enc_d.id\n    -- Find other symbols referenced within that enclosing function\n    JOIN mentions out_m ON out_m.role = 0\n    JOIN chunks out_c ON out_m.chunk_id = out_c.id\n      AND out_c.document_id = enc_der.document_id\n      AND out_c.start_line >= enc_der.start_line\n      AND out_c.end_line <= enc_der.end_line\n    JOIN global_symbols out_gs ON out_m.symbol_id = out_gs.id\n    JOIN defn_enclosing_ranges out_der ON out_gs.id = out_der.symbol_id\n    JOIN documents out_d ON out_der.document_id = out_d.id\n    WHERE ref_m.symbol_id = ? AND ref_m.role = 0\n      AND out_gs.id != ? AND out_gs.id != enc_gs.id\n      AND out_d.id != ref_d.id\n      ${db.symbolNoiseFor('out_gs')}\n      ${db.pathExclusionsFor('out_d')}\n    ORDER BY out_d.relative_path\n    LIMIT 30`,\n    match.symbolId, match.symbolId,\n  );\n\n  const seen = new Set<string>();\n  const connected: SliceResult['connectedSymbols'] = [];\n\n  for (const r of rows) {\n    if (seen.has(r.output_symbol) || db.isIgnored(r.output_file)) continue;\n    seen.add(r.output_symbol);\n    connected.push({\n      symbol: r.output_symbol,\n      shortName: shortenSymbol(r.output_symbol),\n      file: r.output_file,\n      relationship: `used alongside target in ${shortenSymbol(r.enclosing_symbol)}`,\n    });\n  }\n\n  return {\n    symbol: match.symbol,\n    shortName: shortenSymbol(match.symbol),\n    direction: 'forward',\n    connectedSymbols: connected,\n  };\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { RedundantReexport } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find barrel re-exports that no consumer actually imports through.\n *\n * If `queries/index.ts` re-exports `byKind` from `by-kind.ts`, but every\n * consumer of `byKind` imports it directly from `by-kind.ts` (not through\n * `index.ts`), the re-export in the barrel is dead weight.\n *\n * Algorithm:\n * 1. Find all barrel files (index.ts / index.js)\n * 2. For each barrel, find symbols it re-exports (defined elsewhere, referenced in barrel with role=0)\n * 3. For each re-exported symbol, count consumers through the barrel vs direct from the source\n * 4. If zero consumers go through the barrel, the re-export is redundant\n */\nexport function redundantReexports(\n  db: ScipDatabase,\n  opts: { scope?: string; limit?: number } = {},\n): RedundantReexport[] {\n  const { scope, limit } = opts;\n\n  const scopeFilter = scope ? `AND barrel_d.relative_path LIKE '%${scope}%'` : '';\n\n  // Step 1 + 2: Find all barrel files and symbols they re-export.\n  // A re-export is a symbol that:\n  //   - is mentioned in a barrel file with role=0 (reference/import)\n  //   - has its definition (defn_enclosing_ranges) in a DIFFERENT file\n  const reexportRows = db.all<{\n    barrel_doc_id: number;\n    barrel_path: string;\n    symbol_id: number;\n    symbol: string;\n    original_doc_id: number;\n    original_path: string;\n  }>(\n    `SELECT DISTINCT\n      barrel_d.id AS barrel_doc_id,\n      barrel_d.relative_path AS barrel_path,\n      gs.id AS symbol_id,\n      gs.symbol AS symbol,\n      orig_d.id AS original_doc_id,\n      orig_d.relative_path AS original_path\n    FROM mentions m\n    JOIN chunks c ON m.chunk_id = c.id\n    JOIN documents barrel_d ON c.document_id = barrel_d.id\n    JOIN global_symbols gs ON m.symbol_id = gs.id\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents orig_d ON der.document_id = orig_d.id\n    WHERE m.role = 0\n      AND (barrel_d.relative_path LIKE '%/index.ts'\n        OR barrel_d.relative_path LIKE '%/index.js'\n        OR barrel_d.relative_path = 'index.ts'\n        OR barrel_d.relative_path = 'index.js')\n      AND orig_d.id != barrel_d.id\n      ${db.pathExclusionsFor('barrel_d', 'orig_d')}\n      ${db.symbolNoiseFor('gs')}\n      -- Only function-level symbols (ending with ().), not module-level\n      AND gs.symbol LIKE '%().'\n      ${scopeFilter}\n    ORDER BY barrel_d.relative_path, gs.symbol`,\n  );\n\n  const results: RedundantReexport[] = [];\n\n  for (const row of reexportRows) {\n    if (db.isIgnored(row.barrel_path) || db.isIgnored(row.original_path)) continue;\n\n    // Step 3: Count consumers that reference this symbol through the barrel\n    // A \"barrel consumer\" is a file (other than the barrel itself and the original file)\n    // that mentions this symbol AND also mentions something from the barrel document.\n    // More precisely: count distinct files that reference this symbol AND whose\n    // chunk is in a document that also has a role=0 mention pointing to the barrel file's symbols.\n    //\n    // Simpler approach: count distinct documents that reference this symbol (role=0)\n    // grouped by whether the reference chunk is in a file that imports from the barrel\n    // or from the original.\n    //\n    // Actually, the most reliable approach with SCIP data: count how many distinct\n    // consumer documents reference this symbol_id with role=0, excluding the barrel\n    // and the original file themselves. Then check if those consumers also reference\n    // ANY symbol through a mention in the barrel doc vs the original doc.\n    //\n    // Simplest correct approach: In SCIP, when file A does `import { foo } from './bar/index'`,\n    // the mention of `foo` in file A points to the same global symbol regardless of import path.\n    // SCIP doesn't track import provenance. BUT the barrel file itself contains mentions\n    // (role=0 references) of the re-exported symbols. So we can check:\n    // - barrelConsumers: files that mention both this symbol AND any symbol whose definition\n    //   is in the barrel (i.e., they import the barrel)\n    // - directConsumers: files that mention this symbol but don't import the barrel\n    //\n    // Even simpler: check if the barrel document is in the deps of the consumer.\n    // A consumer \"goes through the barrel\" if it has ANY role=0 mention pointing to a\n    // chunk in the barrel file. Otherwise it goes direct.\n\n    const consumerCounts = db.get<{\n      barrel_consumers: number;\n      direct_consumers: number;\n    }>(\n      `SELECT\n        SUM(CASE WHEN uses_barrel = 1 THEN 1 ELSE 0 END) AS barrel_consumers,\n        SUM(CASE WHEN uses_barrel = 0 THEN 1 ELSE 0 END) AS direct_consumers\n      FROM (\n        SELECT\n          consumer_d.id AS consumer_doc_id,\n          MAX(CASE WHEN EXISTS (\n            SELECT 1\n            FROM mentions barrel_m\n            JOIN chunks barrel_c ON barrel_m.chunk_id = barrel_c.id\n            WHERE barrel_c.document_id = consumer_d.id\n              AND barrel_m.role = 0\n              AND barrel_m.symbol_id IN (\n                SELECT m2.symbol_id\n                FROM mentions m2\n                JOIN chunks c2 ON m2.chunk_id = c2.id\n                WHERE c2.document_id = ?\n                  AND m2.role = 0\n              )\n          ) THEN 1 ELSE 0 END) AS uses_barrel\n        FROM mentions ref_m\n        JOIN chunks ref_c ON ref_m.chunk_id = ref_c.id\n        JOIN documents consumer_d ON ref_c.document_id = consumer_d.id\n        WHERE ref_m.symbol_id = ?\n          AND ref_m.role = 0\n          AND consumer_d.id != ?\n          AND consumer_d.id != ?\n          ${db.pathExclusionsFor('consumer_d')}\n        GROUP BY consumer_d.id\n      )`,\n      row.barrel_doc_id,  // for the inner subquery checking barrel mentions\n      row.symbol_id,      // the re-exported symbol\n      row.barrel_doc_id,  // exclude the barrel itself\n      row.original_doc_id, // exclude the original file\n    );\n\n    const barrelConsumers = consumerCounts?.barrel_consumers ?? 0;\n    const directConsumers = consumerCounts?.direct_consumers ?? 0;\n\n    // In TypeScript, `import * as X from './barrel'` resolves all references\n    // directly to the source file — the barrel is transparent to SCIP.\n    // This means barrelConsumers is always 0 for namespace imports.\n    //\n    // We can only confidently report symbols with 0 consumers EVERYWHERE\n    // (both barrel and direct). These are truly dead re-exports.\n    //\n    // Symbols with directConsumers > 0 but barrelConsumers === 0 might be\n    // consumed through a namespace import — we can't tell, so we skip them.\n    if (barrelConsumers === 0 && directConsumers === 0) {\n      results.push({\n        barrelFile: row.barrel_path,\n        symbol: row.symbol,\n        shortName: shortenSymbol(row.symbol),\n        originalFile: row.original_path,\n        barrelConsumers,\n        directConsumers,\n      });\n    }\n  }\n\n  // Sort: symbols with the most direct consumers first (biggest cleanup wins),\n  // then by barrel file path for stable output\n  results.sort((a, b) =>\n    b.directConsumers - a.directConsumers\n    || a.barrelFile.localeCompare(b.barrelFile)\n    || a.shortName.localeCompare(b.shortName),\n  );\n\n  return limit ? results.slice(0, limit) : results;\n}\n","import type { ScipDatabase } from '../db.js';\nimport type { SimilarSignatureGroup } from '../types.js';\nimport { shortenSymbol } from '../symbol-parser.js';\n\n/**\n * Find functions with near-identical type signatures (same parameter types\n * and return type) but different names. These are \"same shape\" functions\n * that may be doing similar work even if their internal implementation differs.\n *\n * The SCIP `documentation` field often contains the full type signature\n * after a `|` delimiter. We parse it, normalize it (strip the function name,\n * whitespace, and case), then group by normalized signature.\n *\n * Groups with 2+ functions = same-shape candidates.\n */\nexport function similarSignatures(\n  db: ScipDatabase,\n  opts: { scope?: string; minLoc?: number; limit?: number } = {},\n): SimilarSignatureGroup[] {\n  const { scope, minLoc = 1, limit } = opts;\n\n  const scopeFilter = scope ? `AND d.relative_path LIKE '%${scope}%'` : '';\n\n  // Get all function-level symbols with their documentation/signature strings.\n  // We use the same signature extraction pattern as symbols.ts / trace.ts.\n  // Filter to symbols that have a documentation field containing '|' (the sig delimiter)\n  // and whose signature contains '(' (indicating a callable).\n  const rows = db.all<{\n    symbol: string;\n    relative_path: string;\n    start_line: number;\n    end_line: number;\n    loc: number;\n    sig: string;\n  }>(\n    `SELECT\n      gs.symbol,\n      d.relative_path,\n      der.start_line,\n      der.end_line,\n      (der.end_line - der.start_line + 1) AS loc,\n      REPLACE(SUBSTR(gs.documentation, INSTR(gs.documentation, '|') + 1), char(10), ' ') AS sig\n    FROM global_symbols gs\n    JOIN defn_enclosing_ranges der ON gs.id = der.symbol_id\n    JOIN documents d ON der.document_id = d.id\n    WHERE gs.documentation IS NOT NULL\n      AND gs.documentation != ''\n      AND INSTR(gs.documentation, '|') > 0\n      AND (der.end_line - der.start_line + 1) >= ?\n      ${db.pathExclusionsFor('d')}\n      ${db.symbolNoiseFor('gs')}\n      ${scopeFilter}\n    ORDER BY d.relative_path, der.start_line`,\n    minLoc,\n  );\n\n  // Group by normalized signature\n  const sigGroups = new Map<string, Array<{\n    symbol: string;\n    shortName: string;\n    file: string;\n    startLine: number;\n    endLine: number;\n    loc: number;\n  }>>();\n\n  for (const row of rows) {\n    if (db.isIgnored(row.relative_path)) continue;\n\n    const normalized = normalizeSignature(row.sig);\n    if (!normalized) continue;\n\n    const entry = {\n      symbol: row.symbol,\n      shortName: shortenSymbol(row.symbol),\n      file: row.relative_path,\n      startLine: row.start_line,\n      endLine: row.end_line,\n      loc: row.loc,\n    };\n\n    const existing = sigGroups.get(normalized);\n    if (existing) {\n      existing.push(entry);\n    } else {\n      sigGroups.set(normalized, [entry]);\n    }\n  }\n\n  // Collect groups with 2+ functions\n  const results: SimilarSignatureGroup[] = [];\n\n  for (const [signature, functions] of sigGroups) {\n    if (functions.length < 2) continue;\n\n    results.push({ signature, functions });\n  }\n\n  // Sort by group size descending (largest groups = most duplication),\n  // then by total LOC in the group\n  results.sort((a, b) => {\n    const sizeDiff = b.functions.length - a.functions.length;\n    if (sizeDiff !== 0) return sizeDiff;\n    const locA = a.functions.reduce((sum, f) => sum + f.loc, 0);\n    const locB = b.functions.reduce((sum, f) => sum + f.loc, 0);\n    return locB - locA;\n  });\n\n  return limit ? results.slice(0, limit) : results;\n}\n\n/**\n * Normalize a signature for comparison:\n * 1. Clean markdown fences and SCIP prefixes\n * 2. Strip everything before the first '(' (removes the function name)\n * 3. Strip whitespace and lowercase\n *\n * Returns null if the signature doesn't contain a callable form.\n */\nfunction normalizeSignature(raw: string): string | null {\n  if (!raw || !raw.trim()) return null;\n\n  // Clean markdown and SCIP decoration (same as cleanSignature)\n  let sig = raw\n    .replace(/^```\\w*\\s*/, '')\n    .replace(/\\s*```$/, '')\n    .replace(/^\\(method\\)\\s*/, '')\n    .replace(/^\\(property\\)\\s*/, '')\n    .replace(/^\\(function\\)\\s*/, '')\n    .replace(/^\\(class\\)\\s*/, '')\n    .replace(/^\\(interface\\)\\s*/, '')\n    .replace(/^\\(enum\\)\\s*/, '')\n    .replace(/^\\(type alias\\)\\s*/, '')\n    .replace(/^\\(const\\)\\s*/, '')\n    .replace(/^\\(var\\)\\s*/, '')\n    .trim();\n\n  // Find the first '(' — everything from there is the parameter/return signature\n  const parenIdx = sig.indexOf('(');\n  if (parenIdx === -1) return null;\n\n  sig = sig.slice(parenIdx);\n\n  // Normalize: strip all whitespace, lowercase\n  sig = sig.replace(/\\s+/g, '').toLowerCase();\n\n  // Must have meaningful content after normalization\n  if (sig.length < 3) return null; // e.g. \"()\" alone is too generic\n\n  return sig;\n}\n","import {\n  existsSync, mkdirSync, symlinkSync, readlinkSync,\n  unlinkSync, chmodSync, createWriteStream,\n} from 'node:fs';\nimport { join, dirname, resolve } from 'node:path';\nimport { homedir, platform, arch } from 'node:os';\nimport { execFileSync } from 'node:child_process';\nimport { fileURLToPath } from 'node:url';\nimport { get as httpsGet } from 'node:https';\nimport { tryInstallScipCli } from './reindex/install.js';\n\nconst IS_WINDOWS = platform() === 'win32';\nconst SKILLS = ['concrete-plan', 'scip-explore', 'scip-debloat', 'scip-verify'];\nconst SCIP_VERSION = 'v0.7.0';\n\n// ── Skills Installation ────────────────────────────────────\n\nexport interface InstallSkillsResult {\n  installed: string[];\n  skipped: string[];\n  alreadyLinked: string[];\n}\n\n/**\n * Install scip-query skills into both Claude Code (~/.claude/skills/)\n * and Codex (~/.codex/skills/). Uses symlinks (junctions on Windows)\n * so skills auto-update when the package updates.\n */\nexport function installSkills(\n  opts: { quiet?: boolean } = {},\n): InstallSkillsResult {\n  const log = opts.quiet ? () => {} : console.log;\n  const thisFile = fileURLToPath(import.meta.url);\n  const skillsSource = resolve(dirname(thisFile), '..', 'skills');\n\n  const targets = [\n    join(homedir(), '.claude', 'skills'),\n    join(homedir(), '.codex', 'skills'),\n  ];\n\n  const result: InstallSkillsResult = {\n    installed: [],\n    skipped: [],\n    alreadyLinked: [],\n  };\n\n  for (const targetDir of targets) {\n    // Only install if the parent directory exists (tool is installed)\n    const parentDir = dirname(targetDir);\n    if (!existsSync(parentDir)) {\n      continue;\n    }\n\n    mkdirSync(targetDir, { recursive: true });\n    const toolName = targetDir.includes('.codex') ? 'Codex' : 'Claude';\n\n    for (const skill of SKILLS) {\n      const source = join(skillsSource, skill);\n      const target = join(targetDir, skill);\n\n      if (!existsSync(source)) {\n        result.skipped.push(`${toolName}/${skill}`);\n        continue;\n      }\n\n      if (existsSync(target)) {\n        try {\n          const existing = readlinkSync(target);\n          if (resolve(existing) === resolve(source)) {\n            result.alreadyLinked.push(`${toolName}/${skill}`);\n            log(`  ok:   ${skill} → ${toolName} (already linked)`);\n            continue;\n          }\n        } catch {\n          // Not a symlink — don't overwrite user's custom skill\n          result.skipped.push(`${toolName}/${skill}`);\n          log(`  skip: ${skill} → ${toolName} (exists, not a symlink)`);\n          continue;\n        }\n        unlinkSync(target);\n      }\n\n      // Use 'junction' on Windows (doesn't need admin), 'dir' elsewhere\n      symlinkSync(source, target, IS_WINDOWS ? 'junction' : 'dir');\n      result.installed.push(`${toolName}/${skill}`);\n      log(`  done: ${skill} → ${toolName}`);\n    }\n  }\n\n  return result;\n}\n\n// ── SCIP CLI Binary Detection & Installation ───────────────\n\n/**\n * Check if the `scip` CLI binary is available on PATH.\n */\nexport function isScipInstalled(): boolean {\n  try {\n    const cmd = IS_WINDOWS ? 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