diff --git a/agents/gsd-intel-updater.md b/agents/gsd-intel-updater.md
index c64ba191d..f238b0988 100644
--- a/agents/gsd-intel-updater.md
+++ b/agents/gsd-intel-updater.md
@@ -57,14 +57,23 @@ The /gsd-intel command has already confirmed that intel.enabled is true before s
 
 ## Project Scope
 
-When analyzing this project, use ONLY canonical source locations:
+**Runtime layout detection (do this first):** Check which runtime root exists by running:
+```bash
+ls -d .kilo 2>/dev/null && echo "kilo" || (ls -d .claude/get-shit-done 2>/dev/null && echo "claude") || echo "unknown"
+```
 
-- `agents/*.md` -- Agent instruction files
-- `commands/gsd/*.md` -- Command files
-- `get-shit-done/bin/` -- CLI tooling
-- `get-shit-done/workflows/` -- Workflow files
-- `get-shit-done/references/` -- Reference docs
-- `hooks/*.js` -- Git hooks
+Use the detected root to resolve all canonical paths below:
+
+| Source type | Standard `.claude` layout | `.kilo` layout |
+|-------------|--------------------------|----------------|
+| Agent files | `agents/*.md` | `.kilo/agents/*.md` |
+| Command files | `commands/gsd/*.md` | `.kilo/command/*.md` |
+| CLI tooling | `get-shit-done/bin/` | `.kilo/get-shit-done/bin/` |
+| Workflow files | `get-shit-done/workflows/` | `.kilo/get-shit-done/workflows/` |
+| Reference docs | `get-shit-done/references/` | `.kilo/get-shit-done/references/` |
+| Hook files | `hooks/*.js` | `.kilo/hooks/*.js` |
+
+When analyzing this project, use ONLY the canonical source locations matching the detected layout. Do not fall back to the standard layout paths if the `.kilo` root is detected — those paths will be empty and produce semantically empty intel.
 
 EXCLUDE from counts and analysis:
 
@@ -72,8 +81,8 @@ EXCLUDE from counts and analysis:
 - `node_modules/`, `dist/`, `build/`, `.git/`
 
 **Count accuracy:** When reporting component counts in stack.json or arch.md, always derive
-counts by running Glob on canonical locations above, not from memory or CLAUDE.md.
-Example: `Glob("agents/*.md")` for agent count.
+counts by running Glob on the layout-resolved canonical locations above, not from memory or CLAUDE.md.
+Example (standard layout): `Glob("agents/*.md")`. Example (kilo): `Glob(".kilo/agents/*.md")`.
 
 ## Forbidden Files
 
diff --git a/tests/bug-2351-intel-kilo-layout.test.cjs b/tests/bug-2351-intel-kilo-layout.test.cjs
new file mode 100644
index 000000000..c305329a9
--- /dev/null
+++ b/tests/bug-2351-intel-kilo-layout.test.cjs
@@ -0,0 +1,77 @@
+/**
+ * Regression test for bug #2351
+ *
+ * gsd-intel-updater used hardcoded canonical paths (`agents/*.md`,
+ * `commands/gsd/*.md`, `hooks/*.js`, etc.) that assumed the standard
+ * `.claude/` runtime layout. Under a `.kilo` install, the runtime root is
+ * `.kilo/`, and the command directory is `command/` (not `commands/gsd/`).
+ * Globs against the old paths returned no results, producing semantically
+ * empty intel files (`"entries": {}`).
+ *
+ * Fix: add runtime layout detection and a mapping table so the agent
+ * resolves paths against the correct root.
+ */
+
+'use strict';
+
+const { test, describe } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('fs');
+const path = require('path');
+
+const AGENT_PATH = path.join(__dirname, '..', 'agents', 'gsd-intel-updater.md');
+
+describe('bug #2351: intel updater kilo layout support', () => {
+  let content;
+
+  test('agent file exists', () => {
+    assert.ok(fs.existsSync(AGENT_PATH), 'agents/gsd-intel-updater.md must exist');
+    content = fs.readFileSync(AGENT_PATH, 'utf-8');
+  });
+
+  test('scope section includes layout detection step', () => {
+    content = content || fs.readFileSync(AGENT_PATH, 'utf-8');
+    const hasDetection =
+      content.includes('ls -d .kilo') ||
+      content.includes('Runtime layout detection') ||
+      content.includes('detected layout') ||
+      content.includes('layout detection');
+    assert.ok(
+      hasDetection,
+      'gsd-intel-updater.md must instruct the agent to detect the runtime layout ' +
+      '(.kilo vs .claude) before resolving canonical paths (#2351)'
+    );
+  });
+
+  test('scope section maps .kilo/agents path', () => {
+    content = content || fs.readFileSync(AGENT_PATH, 'utf-8');
+    assert.ok(
+      content.includes('.kilo/agents'),
+      'scope section must include the .kilo/agents/*.md path so agent count is correct under kilo layout'
+    );
+  });
+
+  test('scope section maps .kilo/command path (not commands/gsd)', () => {
+    content = content || fs.readFileSync(AGENT_PATH, 'utf-8');
+    assert.ok(
+      content.includes('.kilo/command'),
+      'scope section must include .kilo/command path — kilo uses "command/" not "commands/gsd/"'
+    );
+  });
+
+  test('scope section maps .kilo/hooks path', () => {
+    content = content || fs.readFileSync(AGENT_PATH, 'utf-8');
+    assert.ok(
+      content.includes('.kilo/hooks'),
+      'scope section must include .kilo/hooks path for hook file counts'
+    );
+  });
+
+  test('scope section retains standard layout paths for .claude installs', () => {
+    content = content || fs.readFileSync(AGENT_PATH, 'utf-8');
+    assert.ok(
+      content.includes('agents/*.md') || content.includes('Standard `.claude` layout'),
+      'scope section must still document the standard .claude layout paths for non-kilo installs'
+    );
+  });
+});