feat(intel): add Stop hook to prune deleted files

New intel-prune.js hook runs after each Claude response.
Checks if indexed files still exist, removes stale entries.

Fast (only fs.existsSync checks) and silent (never blocks).

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

bin/install.js

@@ -456,6 +456,29 @@ function install(isGlobal) {
     console.log(`  ${green}✓${reset} Configured intel session hook`);
   }
 
+  // Stop hook for pruning deleted files
+  const intelPruneCommand = isGlobal
+    ? 'node "$HOME/.claude/hooks/intel-prune.js"'
+    : 'node .claude/hooks/intel-prune.js';
+
+  if (!settings.hooks.Stop) {
+    settings.hooks.Stop = [];
+  }
+
+  const hasIntelPruneHook = settings.hooks.Stop.some(entry =>
+    entry.hooks && entry.hooks.some(h => h.command && h.command.includes('intel-prune'))
+  );
+
+  if (!hasIntelPruneHook) {
+    settings.hooks.Stop.push({
+      hooks: [{
+        type: 'command',
+        command: intelPruneCommand
+      }]
+    });
+    console.log(`  ${green}✓${reset} Configured intel prune hook`);
+  }
+
   return { settingsPath, settings, statuslineCommand };
 }
 

hooks/intel-prune.js

@@ -0,0 +1,78 @@
+#!/usr/bin/env node
+
+/**
+ * Intel Prune Hook (Stop event)
+ *
+ * Removes stale entries from index.json when files no longer exist.
+ * Runs after each Claude response to keep intel fresh.
+ *
+ * Fast: Only does fs.existsSync checks, no file reading.
+ * Silent: Never blocks or errors, always exits 0.
+ */
+
+const fs = require('fs');
+const path = require('path');
+
+function pruneIndex() {
+  const intelDir = path.join(process.cwd(), '.planning', 'intel');
+  const indexPath = path.join(intelDir, 'index.json');
+
+  // Only run if intel directory exists (opt-in check)
+  if (!fs.existsSync(intelDir)) {
+    return { pruned: 0, total: 0 };
+  }
+
+  // Read existing index
+  let index;
+  try {
+    const content = fs.readFileSync(indexPath, 'utf8');
+    index = JSON.parse(content);
+  } catch (e) {
+    // No index or invalid JSON
+    return { pruned: 0, total: 0 };
+  }
+
+  if (!index.files || typeof index.files !== 'object') {
+    return { pruned: 0, total: 0 };
+  }
+
+  // Check each file and collect deleted ones
+  const filePaths = Object.keys(index.files);
+  const deleted = filePaths.filter(filePath => !fs.existsSync(filePath));
+
+  if (deleted.length === 0) {
+    return { pruned: 0, total: filePaths.length };
+  }
+
+  // Remove deleted entries
+  for (const filePath of deleted) {
+    delete index.files[filePath];
+  }
+  index.updated = Date.now();
+
+  // Write updated index
+  fs.writeFileSync(indexPath, JSON.stringify(index, null, 2));
+
+  // Regenerate conventions and summary after pruning
+  // Import detection logic from intel-index.js would be complex,
+  // so we just update the index. Conventions/summary stay until
+  // next PostToolUse or /gsd:analyze-codebase refresh.
+
+  return { pruned: deleted.length, total: filePaths.length };
+}
+
+// Read JSON from stdin (standard hook pattern)
+let input = '';
+process.stdin.setEncoding('utf8');
+process.stdin.on('data', chunk => input += chunk);
+process.stdin.on('end', () => {
+  try {
+    // Stop hook receives session data, but we don't need it
+    // Just prune stale entries
+    pruneIndex();
+    process.exit(0);
+  } catch (error) {
+    // Silent failure - never block Claude
+    process.exit(0);
+  }
+});