feat: add file limit to structure tool

.github/workflows/benchmark.yml

@@ -28,8 +28,10 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: "22"
+          cache: "npm"
 
-      - run: npm install
+      - name: Install dependencies
+        run: npm ci --prefer-offline --no-audit --no-fund
 
       - name: Run build benchmark
         run: node scripts/benchmark.js 2>/dev/null > benchmark-result.json
@@ -91,8 +93,10 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: "22"
+          cache: "npm"
 
-      - run: npm install
+      - name: Install dependencies
+        run: npm ci --prefer-offline --no-audit --no-fund
 
       - name: Cache HuggingFace models
         uses: actions/cache@v4
@@ -166,8 +170,10 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: "22"
+          cache: "npm"
 
-      - run: npm install
+      - name: Install dependencies
+        run: npm ci --prefer-offline --no-audit --no-fund
 
       - name: Run query benchmark
         run: node scripts/query-benchmark.js 2>/dev/null > query-benchmark-result.json
@@ -229,8 +235,10 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: "22"
+          cache: "npm"
 
-      - run: npm install
+      - name: Install dependencies
+        run: npm ci --prefer-offline --no-audit --no-fund
 
       - name: Run incremental benchmark
         run: node scripts/incremental-benchmark.js 2>/dev/null > incremental-benchmark-result.json

src/cli.js

@@ -502,6 +502,7 @@ program
   .option('-d, --db <path>', 'Path to graph.db')
   .option('--depth <n>', 'Max directory depth')
   .option('--sort <metric>', 'Sort by: cohesion | fan-in | fan-out | density | files', 'files')
+  .option('--full', 'Show all files without limit')
   .option('-T, --no-tests', 'Exclude test/spec files')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
@@ -511,6 +512,7 @@ program
       directory: dir,
       depth: opts.depth ? parseInt(opts.depth, 10) : undefined,
       sort: opts.sort,
+      full: opts.full,
       noTests: resolveNoTests(opts),
     });
     if (opts.json) {

src/mcp.js

@@ -259,7 +259,7 @@ const BASE_TOOLS = [
   {
     name: 'structure',
     description:
-      'Show project structure with directory hierarchy, cohesion scores, and per-file metrics',
+      'Show project structure with directory hierarchy, cohesion scores, and per-file metrics. Per-file details are capped at 25 files by default; use full=true to show all.',
     inputSchema: {
       type: 'object',
       properties: {
@@ -270,6 +270,11 @@ const BASE_TOOLS = [
           enum: ['cohesion', 'fan-in', 'fan-out', 'density', 'files'],
           description: 'Sort directories by metric',
         },
+        full: {
+          type: 'boolean',
+          description: 'Return all files without limit',
+          default: false,
+        },
       },
     },
   },
@@ -571,6 +576,7 @@ export async function startMCPServer(customDbPath, options = {}) {
             directory: args.directory,
             depth: args.depth,
             sort: args.sort,
+            full: args.full,
           });
           break;
         }

src/structure.js

@@ -330,6 +330,8 @@ export function structureData(customDbPath, opts = {}) {
   const maxDepth = opts.depth || null;
   const sortBy = opts.sort || 'files';
   const noTests = opts.noTests || false;
+  const full = opts.full || false;
+  const fileLimit = opts.fileLimit || 25;
 
   // Get all directory nodes with their metrics
   let dirs = db
@@ -403,6 +405,33 @@ export function structureData(customDbPath, opts = {}) {
   });
 
   db.close();
+
+  // Apply global file limit unless full mode
+  if (!full) {
+    const totalFiles = result.reduce((sum, d) => sum + d.files.length, 0);
+    if (totalFiles > fileLimit) {
+      let shown = 0;
+      for (const d of result) {
+        const remaining = fileLimit - shown;
+        if (remaining <= 0) {
+          d.files = [];
+        } else if (d.files.length > remaining) {
+          d.files = d.files.slice(0, remaining);
+          shown = fileLimit;
+        } else {
+          shown += d.files.length;
+        }
+      }
+      const suppressed = totalFiles - fileLimit;
+      return {
+        directories: result,
+        count: result.length,
+        suppressed,
+        warning: `${suppressed} files omitted (showing ${fileLimit}/${totalFiles}). Use --full to show all files, or narrow with --directory.`,
+      };
+    }
+  }
+
   return { directories: result, count: result.length };
 }
 
@@ -539,6 +568,10 @@ export function formatStructure(data) {
       );
     }
   }
+  if (data.warning) {
+    lines.push('');
+    lines.push(`⚠ ${data.warning}`);
+  }
   return lines.join('\n');
 }
 

tests/integration/structure.test.js

@@ -133,6 +133,33 @@ describe('structureData', () => {
   });
 });
 
+describe('structureData file limit', () => {
+  test('default fileLimit truncates files and includes warning when exceeded', () => {
+    // Use a very low fileLimit to trigger truncation on the small fixture
+    const data = structureData(dbPath, { fileLimit: 2 });
+    const shownFiles = data.directories.reduce((sum, d) => sum + d.files.length, 0);
+    expect(shownFiles).toBeLessThanOrEqual(2);
+    expect(data.suppressed).toBeGreaterThan(0);
+    expect(data.warning).toMatch(/files omitted/);
+    expect(data.warning).toMatch(/--full/);
+  });
+
+  test('full: true returns all files without warning', () => {
+    const data = structureData(dbPath, { full: true });
+    const totalFiles = data.directories.reduce((sum, d) => sum + d.files.length, 0);
+    expect(totalFiles).toBeGreaterThan(0);
+    expect(data.suppressed).toBeUndefined();
+    expect(data.warning).toBeUndefined();
+  });
+
+  test('no truncation when total files are within limit', () => {
+    // fileLimit higher than total files should not add warning
+    const data = structureData(dbPath, { fileLimit: 100 });
+    expect(data.suppressed).toBeUndefined();
+    expect(data.warning).toBeUndefined();
+  });
+});
+
 describe('hotspotsData', () => {
   test('returns file hotspots ranked by fan-in', () => {
     const data = hotspotsData(dbPath, { metric: 'fan-in', level: 'file', limit: 5 });