diff --git a/src/cli.js b/src/cli.js
index ccf8fbc47..4700ebfd2 100644
--- a/src/cli.js
+++ b/src/cli.js
@@ -395,8 +395,15 @@ registry
   .command('prune')
   .description('Remove stale registry entries (missing directories or idle beyond TTL)')
   .option('--ttl <days>', 'Days of inactivity before pruning (default: 30)', '30')
+  .option('--exclude <names>', 'Comma-separated repo names to preserve from pruning')
   .action((opts) => {
-    const pruned = pruneRegistry(undefined, parseInt(opts.ttl, 10));
+    const excludeNames = opts.exclude
+      ? opts.exclude
+          .split(',')
+          .map((s) => s.trim())
+          .filter((s) => s.length > 0)
+      : [];
+    const pruned = pruneRegistry(undefined, parseInt(opts.ttl, 10), excludeNames);
     if (pruned.length === 0) {
       console.log('No stale entries found.');
     } else {
@@ -464,6 +471,7 @@ program
   .option('-k, --kind <kind>', 'Filter by kind: function, method, class')
   .option('--file <pattern>', 'Filter by file path pattern')
   .option('--rrf-k <number>', 'RRF k parameter for multi-query ranking', '60')
+  .option('-j, --json', 'Output as JSON')
   .action(async (query, opts) => {
     await search(query, opts.db, {
       limit: parseInt(opts.limit, 10),
@@ -473,6 +481,7 @@ program
       kind: opts.kind,
       filePattern: opts.file,
       rrfK: parseInt(opts.rrfK, 10),
+      json: opts.json,
     });
   });
 
diff --git a/src/embedder.js b/src/embedder.js
index 20882e9bc..b0e0588ca 100644
--- a/src/embedder.js
+++ b/src/embedder.js
@@ -16,6 +16,28 @@ function splitIdentifier(name) {
     .trim();
 }
 
+/**
+ * Match a file path against a glob pattern.
+ * Supports *, **, and ? wildcards. Zero dependencies.
+ */
+function globMatch(filePath, pattern) {
+  // Normalize separators to forward slashes
+  const normalized = filePath.replace(/\\/g, '/');
+  // Escape regex specials except glob chars
+  let regex = pattern.replace(/\\/g, '/').replace(/[.+^${}()|[\]\\]/g, '\\$&');
+  // Replace ** first (matches any path segment), then * and ?
+  regex = regex.replace(/\*\*/g, '\0');
+  regex = regex.replace(/\*/g, '[^/]*');
+  regex = regex.replace(/\0/g, '.*');
+  regex = regex.replace(/\?/g, '[^/]');
+  try {
+    return new RegExp(`^${regex}$`).test(normalized);
+  } catch {
+    // Malformed pattern — fall back to substring match
+    return normalized.includes(pattern);
+  }
+}
+
 // Lazy-load transformers (heavy, optional module)
 let pipeline = null;
 let _cos_sim = null;
@@ -496,7 +518,8 @@ function _prepareSearch(customDbPath, opts = {}) {
     conditions.push('n.kind = ?');
     params.push(opts.kind);
   }
-  if (opts.filePattern) {
+  const isGlob = opts.filePattern && /[*?[\]]/.test(opts.filePattern);
+  if (opts.filePattern && !isGlob) {
     conditions.push('n.file LIKE ?');
     params.push(`%${opts.filePattern}%`);
   }
@@ -505,6 +528,9 @@ function _prepareSearch(customDbPath, opts = {}) {
   }
 
   let rows = db.prepare(sql).all(...params);
+  if (isGlob) {
+    rows = rows.filter((row) => globMatch(row.file, opts.filePattern));
+  }
   if (noTests) {
     rows = rows.filter((row) => !TEST_PATTERN.test(row.file));
   }
@@ -668,6 +694,11 @@ export async function search(query, customDbPath, opts = {}) {
     const data = await searchData(singleQuery, customDbPath, opts);
     if (!data) return;
 
+    if (opts.json) {
+      console.log(JSON.stringify(data, null, 2));
+      return;
+    }
+
     console.log(`\nSemantic search: "${singleQuery}"\n`);
 
     if (data.results.length === 0) {
@@ -687,6 +718,11 @@ export async function search(query, customDbPath, opts = {}) {
     const data = await multiSearchData(queries, customDbPath, opts);
     if (!data) return;
 
+    if (opts.json) {
+      console.log(JSON.stringify(data, null, 2));
+      return;
+    }
+
     console.log(`\nMulti-query semantic search (RRF, k=${opts.rrfK || 60}):`);
     queries.forEach((q, i) => {
       console.log(`  [${i + 1}] "${q}"`);
diff --git a/src/registry.js b/src/registry.js
index caa970e8c..33acc8c75 100644
--- a/src/registry.js
+++ b/src/registry.js
@@ -136,12 +136,20 @@ export function resolveRepoDbPath(name, registryPath = REGISTRY_PATH) {
  * or that haven't been accessed within `ttlDays` days.
  * Returns an array of `{ name, path, reason }` for each pruned entry.
  */
-export function pruneRegistry(registryPath = REGISTRY_PATH, ttlDays = DEFAULT_TTL_DAYS) {
+export function pruneRegistry(
+  registryPath = REGISTRY_PATH,
+  ttlDays = DEFAULT_TTL_DAYS,
+  excludeNames = [],
+) {
   const registry = loadRegistry(registryPath);
   const pruned = [];
   const cutoff = Date.now() - ttlDays * 24 * 60 * 60 * 1000;
+  const excludeSet = new Set(
+    excludeNames.filter((n) => typeof n === 'string' && n.trim().length > 0),
+  );
 
   for (const [name, entry] of Object.entries(registry.repos)) {
+    if (excludeSet.has(name)) continue;
     if (!fs.existsSync(entry.path)) {
       pruned.push({ name, path: entry.path, reason: 'missing' });
       delete registry.repos[name];
diff --git a/tests/search/embedder-search.test.js b/tests/search/embedder-search.test.js
index 8af53953a..bbe57b674 100644
--- a/tests/search/embedder-search.test.js
+++ b/tests/search/embedder-search.test.js
@@ -220,6 +220,24 @@ describe('multiSearchData', () => {
   });
 });
 
+describe('searchData file pattern', () => {
+  test('glob src/*.js matches only direct children of src/', async () => {
+    const data = await searchData('auth', dbPath, { minScore: 0.01, filePattern: 'src/*.js' });
+    expect(data).not.toBeNull();
+    for (const r of data.results) {
+      expect(r.file).toMatch(/^src\/[^/]+\.js$/);
+    }
+  });
+
+  test('plain substring auth still works (backward compat)', async () => {
+    const data = await searchData('auth', dbPath, { minScore: 0.01, filePattern: 'auth' });
+    expect(data).not.toBeNull();
+    for (const r of data.results) {
+      expect(r.file).toContain('auth');
+    }
+  });
+});
+
 describe('search (CLI wrapper)', () => {
   /** Capture console.log calls and return joined output. */
   function captureLog(fn) {
@@ -253,4 +271,22 @@ describe('search (CLI wrapper)', () => {
     expect(out).toContain('Semantic search: "auth"');
     expect(out).not.toContain('Multi-query');
   });
+
+  test('single query with json: true outputs valid JSON with results array', async () => {
+    const out = await captureLog(() => search('auth', dbPath, { minScore: 0.2, json: true }));
+    const parsed = JSON.parse(out);
+    expect(parsed.results).toBeInstanceOf(Array);
+    expect(parsed.results.length).toBeGreaterThan(0);
+    expect(parsed.results[0]).toHaveProperty('similarity');
+    expect(parsed.results[0]).toHaveProperty('name');
+  });
+
+  test('multi query with json: true outputs valid JSON with rrf and queryScores', async () => {
+    const out = await captureLog(() => search('auth ; jwt', dbPath, { minScore: 0.2, json: true }));
+    const parsed = JSON.parse(out);
+    expect(parsed.results).toBeInstanceOf(Array);
+    expect(parsed.results.length).toBeGreaterThan(0);
+    expect(parsed.results[0]).toHaveProperty('rrf');
+    expect(parsed.results[0]).toHaveProperty('queryScores');
+  });
 });
diff --git a/tests/unit/registry.test.js b/tests/unit/registry.test.js
index 7623ba8f2..d70c95a26 100644
--- a/tests/unit/registry.test.js
+++ b/tests/unit/registry.test.js
@@ -454,6 +454,71 @@ describe('pruneRegistry', () => {
     const pruned = pruneRegistry(registryPath);
     expect(pruned).toEqual([]);
   });
+
+  it('excluded entry survives missing-dir prune', () => {
+    const dir1 = path.join(tmpDir, 'keep');
+    const dir2 = path.join(tmpDir, 'gone-excluded');
+    fs.mkdirSync(dir1, { recursive: true });
+    fs.mkdirSync(dir2, { recursive: true });
+
+    registerRepo(dir1, 'keep', registryPath);
+    registerRepo(dir2, 'gone-excluded', registryPath);
+
+    // Remove the directory
+    fs.rmSync(dir2, { recursive: true, force: true });
+
+    const pruned = pruneRegistry(registryPath, 30, ['gone-excluded']);
+    expect(pruned).toHaveLength(0);
+
+    const reg = loadRegistry(registryPath);
+    expect(reg.repos['gone-excluded']).toBeDefined();
+  });
+
+  it('excluded entry survives TTL prune', () => {
+    const dir = path.join(tmpDir, 'protected');
+    fs.mkdirSync(dir, { recursive: true });
+
+    const oldDate = new Date(Date.now() - 60 * 24 * 60 * 60 * 1000).toISOString();
+    const registry = {
+      repos: {
+        protected: {
+          path: dir,
+          dbPath: path.join(dir, '.codegraph', 'graph.db'),
+          addedAt: oldDate,
+          lastAccessedAt: oldDate,
+        },
+      },
+    };
+    saveRegistry(registry, registryPath);
+
+    const pruned = pruneRegistry(registryPath, 30, ['protected']);
+    expect(pruned).toHaveLength(0);
+
+    const reg = loadRegistry(registryPath);
+    expect(reg.repos.protected).toBeDefined();
+  });
+
+  it('empty exclude array prunes normally (backward compat)', () => {
+    const dir = path.join(tmpDir, 'stale');
+    fs.mkdirSync(dir, { recursive: true });
+
+    const oldDate = new Date(Date.now() - 60 * 24 * 60 * 60 * 1000).toISOString();
+    const registry = {
+      repos: {
+        stale: {
+          path: dir,
+          dbPath: path.join(dir, '.codegraph', 'graph.db'),
+          addedAt: oldDate,
+          lastAccessedAt: oldDate,
+        },
+      },
+    };
+    saveRegistry(registry, registryPath);
+
+    const pruned = pruneRegistry(registryPath, 30, []);
+    expect(pruned).toHaveLength(1);
+    expect(pruned[0].name).toBe('stale');
+  });
 });
 
 // ─── DEFAULT_TTL_DAYS ──────────────────────────────────────────────
diff --git a/vitest.config.js b/vitest.config.js
index 97575fa9b..a92ad038c 100644
--- a/vitest.config.js
+++ b/vitest.config.js
@@ -4,5 +4,6 @@ export default defineConfig({
   test: {
     globals: true,
     testTimeout: 30000,
+    exclude: ['**/node_modules/**', '**/.git/**', '.claude/**'],
   },
 });