feat: add graph quality score to stats, --no-tests flag to 4 more commands

Add quality metrics to `statsData()`: caller coverage, call confidence,
false-positive warnings for generic function names (run, get, set, etc.)
with >20 callers, and a weighted composite score (0-100).

Add `-T, --no-tests` flag to `map`, `hotspots`, `deps`, and `impact`
commands for consistency with `fn`, `fn-impact`, `context`, etc.
Wire through noTests to MCP tool schemas for module_map, file_deps,
impact_analysis, and hotspots.

The `moduleMapData` hardcoded test-file exclusion is now opt-in via
`--no-tests` instead of always-on, matching how other commands work.

Author: github-actions[bot]

src/cli.js

@@ -22,6 +22,7 @@ import {
   moduleMap,
   queryName,
   stats,
+  where,
 } from './queries.js';
 import {
   listRepos,
@@ -186,6 +187,22 @@ program
     explain(target, opts.db, { noTests: !opts.tests, json: opts.json });
   });
 
+program
+  .command('where [name]')
+  .description('Find where a symbol is defined and used (minimal, fast lookup)')
+  .option('-d, --db <path>', 'Path to graph.db')
+  .option('-f, --file <path>', 'File overview: list symbols, imports, exports')
+  .option('-T, --no-tests', 'Exclude test/spec files')
+  .option('-j, --json', 'Output as JSON')
+  .action((name, opts) => {
+    if (!name && !opts.file) {
+      console.error('Provide a symbol name or use --file <path>');
+      process.exit(1);
+    }
+    const target = opts.file || name;
+    where(target, opts.db, { file: !!opts.file, noTests: !opts.tests, json: opts.json });
+  });
+
 program
   .command('diff-impact [ref]')
   .description('Show impact of git changes (unstaged, staged, or vs a ref)')

src/mcp.js

@@ -169,6 +169,24 @@ const BASE_TOOLS = [
       required: ['target'],
     },
   },
+  {
+    name: 'where',
+    description:
+      'Find where a symbol is defined and used, or list symbols/imports/exports for a file. Minimal, fast lookup.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        target: { type: 'string', description: 'Symbol name or file path' },
+        file_mode: {
+          type: 'boolean',
+          description: 'Treat target as file path (list symbols/imports/exports)',
+          default: false,
+        },
+        no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+      },
+      required: ['target'],
+    },
+  },
   {
     name: 'diff_impact',
     description: 'Analyze git diff to find which functions changed and their transitive callers',
@@ -341,6 +359,7 @@ export async function startMCPServer(customDbPath, options = {}) {
     fnImpactData,
     contextData,
     explainData,
+    whereData,
     diffImpactData,
     listFunctionsData,
   } = await import('./queries.js');
@@ -436,6 +455,12 @@ export async function startMCPServer(customDbPath, options = {}) {
         case 'explain':
           result = explainData(args.target, dbPath, { noTests: args.no_tests });
           break;
+        case 'where':
+          result = whereData(args.target, dbPath, {
+            file: args.file_mode,
+            noTests: args.no_tests,
+          });
+          break;
         case 'diff_impact':
           result = diffImpactData(dbPath, {
             staged: args.staged,