diff --git a/README.md b/README.md
index 095c20e4..2a13efc6 100644
--- a/README.md
+++ b/README.md
@@ -117,7 +117,9 @@ Verify with:
 - Cline: GSD installs via `.clinerules` — verify by checking `.clinerules` exists
 
 > [!NOTE]
-> Claude Code 2.1.88+, Qwen Code, and Codex install as skills (`skills/gsd-*/SKILL.md`). Older Claude Code versions use `commands/gsd/`. Cline uses `.clinerules` for configuration. The installer handles all formats automatically.
+> Claude Code 2.1.88+, Qwen Code, and Codex install as skills (`.claude/skills/`, `./.codex/skills/`, or the matching global `~/.claude/skills/` / `~/.codex/skills/` roots). Older Claude Code versions use `commands/gsd/`. `~/.claude/get-shit-done/skills/` is import-only for legacy migration. The installer handles all formats automatically.
+
+The canonical discovery contract is documented in [docs/skills/discovery-contract.md](docs/skills/discovery-contract.md).
 
 > [!TIP]
 > For source-based installs or environments where npm is unavailable, see **[docs/manual-update.md](docs/manual-update.md)**.
@@ -818,8 +820,9 @@ This prevents Claude from reading these files entirely, regardless of what comma
 
 **Commands not found after install?**
 - Restart your runtime to reload commands/skills
-- Verify files exist in `~/.claude/skills/gsd-*/SKILL.md` (Claude Code 2.1.88+) or `~/.claude/commands/gsd/` (legacy)
-- For Codex, verify skills exist in `~/.codex/skills/gsd-*/SKILL.md` (global) or `./.codex/skills/gsd-*/SKILL.md` (local)
+- Verify files exist in `~/.claude/skills/gsd-*/SKILL.md` or `~/.codex/skills/gsd-*/SKILL.md` for managed global installs
+- For local installs, verify `.claude/skills/gsd-*/SKILL.md` or `./.codex/skills/gsd-*/SKILL.md`
+- Legacy Claude Code installs still use `~/.claude/commands/gsd/`
 
 **Commands not working as expected?**
 - Run `/gsd-help` to verify installation
diff --git a/docs/skills/discovery-contract.md b/docs/skills/discovery-contract.md
new file mode 100644
index 00000000..6bbbb228
--- /dev/null
+++ b/docs/skills/discovery-contract.md
@@ -0,0 +1,92 @@
+# Skill Discovery Contract
+
+> Canonical rules for scanning, inventorying, and rendering GSD skills.
+
+## Root Categories
+
+### Project Roots
+
+Scan these roots relative to the project root:
+
+- `.claude/skills/`
+- `.agents/skills/`
+- `.cursor/skills/`
+- `.github/skills/`
+- `./.codex/skills/`
+
+These roots are used for project-specific skills and for the project `CLAUDE.md` skills section.
+
+### Managed Global Roots
+
+Scan these roots relative to the user home directory:
+
+- `~/.claude/skills/`
+- `~/.codex/skills/`
+
+These roots are used for managed runtime installs and inventory reporting.
+
+### Deprecated Import-Only Root
+
+- `~/.claude/get-shit-done/skills/`
+
+This root is kept for legacy migration only. Inventory code may report it, but new installs should not write here.
+
+### Legacy Claude Commands
+
+- `~/.claude/commands/gsd/`
+
+This is not a skills root. Discovery code only checks whether it exists so inventory can report legacy Claude installs.
+
+## Normalization Rules
+
+- Scan only subdirectories that contain `SKILL.md`.
+- Read `name` and `description` from YAML frontmatter.
+- Use the directory name when `name` is missing.
+- Extract trigger hints from body lines that match `TRIGGER when: ...`.
+- Treat `gsd-*` directories as installed framework skills.
+- Treat `~/.claude/get-shit-done/skills/` entries as deprecated/import-only.
+- Treat `~/.claude/commands/gsd/` as legacy command installation metadata, not skills.
+
+## Scanner Behavior
+
+### `sdk/src/query/skills.ts`
+
+- Returns a de-duplicated list of discovered skill names.
+- Scans project roots plus managed global roots.
+- Does not scan the deprecated import-only root.
+
+### `get-shit-done/bin/lib/profile-output.cjs`
+
+- Builds the project `CLAUDE.md` skills section.
+- Scans project roots only.
+- Skips `gsd-*` directories so the project section stays focused on user/project skills.
+- Adds `.codex/skills/` to the project discovery set.
+
+### `get-shit-done/bin/lib/init.cjs`
+
+- Generates the skill inventory object for `skill-manifest`.
+- Reports `skills`, `roots`, `installation`, and `counts`.
+- Marks `gsd_skills_installed` when any discovered skill name starts with `gsd-`.
+- Marks `legacy_claude_commands_installed` when `~/.claude/commands/gsd/` contains `.md` command files.
+
+## Inventory Shape
+
+`skill-manifest` returns a JSON object with:
+
+- `skills`: normalized skill entries
+- `roots`: the canonical roots that were checked
+- `installation`: summary booleans for installed GSD skills and legacy Claude commands
+- `counts`: small inventory counts for downstream consumers
+
+Each skill entry includes:
+
+- `name`
+- `description`
+- `triggers`
+- `path`
+- `file_path`
+- `root`
+- `scope`
+- `installed`
+- `deprecated`
+
diff --git a/get-shit-done/bin/lib/init.cjs b/get-shit-done/bin/lib/init.cjs
index 8a704b81..b00b9b3d 100644
--- a/get-shit-done/bin/lib/init.cjs
+++ b/get-shit-done/bin/lib/init.cjs
@@ -1590,75 +1590,207 @@ function cmdAgentSkills(cwd, agentType, raw) {
 /**
  * Generate a skill manifest from a skills directory.
  *
- * Scans the given skills directory for subdirectories containing SKILL.md,
- * extracts frontmatter (name, description) and trigger conditions from the
- * body text, and returns an array of skill descriptors.
+ * Scans the canonical skill discovery roots and returns a normalized
+ * inventory object with discovered skills, root metadata, and installation
+ * summary flags. A legacy `skillsDir` override is still accepted for focused
+ * scans, but the default mode is multi-root discovery.
  *
- * @param {string} skillsDir - Absolute path to the skills directory
- * @returns {Array<{name: string, description: string, triggers: string[], path: string}>}
+ * @param {string} cwd - Project root directory
+ * @param {string|null} [skillsDir] - Optional absolute path to a specific skills directory
+ * @returns {{
+ *   skills: Array<{name: string, description: string, triggers: string[], path: string, file_path: string, root: string, scope: string, installed: boolean, deprecated: boolean}>,
+ *   roots: Array<{root: string, path: string, scope: string, present: boolean, skill_count?: number, command_count?: number, deprecated?: boolean}>,
+ *   installation: { gsd_skills_installed: boolean, legacy_claude_commands_installed: boolean },
+ *   counts: { skills: number, roots: number }
+ * }}
  */
-function buildSkillManifest(skillsDir) {
+function buildSkillManifest(cwd, skillsDir = null) {
   const { extractFrontmatter } = require('./frontmatter.cjs');
+  const os = require('os');
 
-  if (!fs.existsSync(skillsDir)) return [];
+  const canonicalRoots = skillsDir ? [{
+    root: path.resolve(skillsDir),
+    path: path.resolve(skillsDir),
+    scope: 'custom',
+    present: fs.existsSync(skillsDir),
+    kind: 'skills',
+  }] : [
+    {
+      root: '.claude/skills',
+      path: path.join(cwd, '.claude', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '.agents/skills',
+      path: path.join(cwd, '.agents', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '.cursor/skills',
+      path: path.join(cwd, '.cursor', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '.github/skills',
+      path: path.join(cwd, '.github', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '.codex/skills',
+      path: path.join(cwd, '.codex', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '~/.claude/skills',
+      path: path.join(os.homedir(), '.claude', 'skills'),
+      scope: 'global',
+      kind: 'skills',
+    },
+    {
+      root: '~/.codex/skills',
+      path: path.join(os.homedir(), '.codex', 'skills'),
+      scope: 'global',
+      kind: 'skills',
+    },
+    {
+      root: '~/.claude/get-shit-done/skills',
+      path: path.join(os.homedir(), '.claude', 'get-shit-done', 'skills'),
+      scope: 'import-only',
+      kind: 'skills',
+      deprecated: true,
+    },
+    {
+      root: '~/.claude/commands/gsd',
+      path: path.join(os.homedir(), '.claude', 'commands', 'gsd'),
+      scope: 'legacy-commands',
+      kind: 'commands',
+      deprecated: true,
+    },
+  ];
 
-  let entries;
-  try {
-    entries = fs.readdirSync(skillsDir, { withFileTypes: true });
-  } catch {
-    return [];
-  }
+  const skills = [];
+  const roots = [];
+  let legacyClaudeCommandsInstalled = false;
+  for (const rootInfo of canonicalRoots) {
+    const rootPath = rootInfo.path;
+    const rootSummary = {
+      root: rootInfo.root,
+      path: rootPath,
+      scope: rootInfo.scope,
+      present: fs.existsSync(rootPath),
+      deprecated: !!rootInfo.deprecated,
+    };
 
-  const manifest = [];
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-
-    const skillMdPath = path.join(skillsDir, entry.name, 'SKILL.md');
-    if (!fs.existsSync(skillMdPath)) continue;
-
-    let content;
-    try {
-      content = fs.readFileSync(skillMdPath, 'utf-8');
-    } catch {
+    if (!rootSummary.present) {
+      roots.push(rootSummary);
       continue;
     }
 
-    const frontmatter = extractFrontmatter(content);
-    const name = frontmatter.name || entry.name;
-    const description = frontmatter.description || '';
-
-    // Extract trigger lines from body text (after frontmatter)
-    const triggers = [];
-    const bodyMatch = content.match(/^---[\s\S]*?---\s*\n([\s\S]*)$/);
-    if (bodyMatch) {
-      const body = bodyMatch[1];
-      const triggerLines = body.match(/^TRIGGER\s+when:\s*(.+)$/gmi);
-      if (triggerLines) {
-        for (const line of triggerLines) {
-          const m = line.match(/^TRIGGER\s+when:\s*(.+)$/i);
-          if (m) triggers.push(m[1].trim());
-        }
+    if (rootInfo.kind === 'commands') {
+      let entries = [];
+      try {
+        entries = fs.readdirSync(rootPath, { withFileTypes: true });
+      } catch {
+        roots.push(rootSummary);
+        continue;
       }
+
+      const commandFiles = entries.filter(entry => entry.isFile() && entry.name.endsWith('.md'));
+      rootSummary.command_count = commandFiles.length;
+      if (rootSummary.command_count > 0) legacyClaudeCommandsInstalled = true;
+      roots.push(rootSummary);
+      continue;
     }
 
-    manifest.push({
-      name,
-      description,
-      triggers,
-      path: entry.name,
-    });
+    let entries;
+    try {
+      entries = fs.readdirSync(rootPath, { withFileTypes: true });
+    } catch {
+      roots.push(rootSummary);
+      continue;
+    }
+
+    let skillCount = 0;
+    for (const entry of entries) {
+      if (!entry.isDirectory()) continue;
+
+      const skillMdPath = path.join(rootPath, entry.name, 'SKILL.md');
+      if (!fs.existsSync(skillMdPath)) continue;
+
+      let content;
+      try {
+        content = fs.readFileSync(skillMdPath, 'utf-8');
+      } catch {
+        continue;
+      }
+
+      const frontmatter = extractFrontmatter(content);
+      const name = frontmatter.name || entry.name;
+      const description = frontmatter.description || '';
+
+      // Extract trigger lines from body text (after frontmatter)
+      const triggers = [];
+      const bodyMatch = content.match(/^---[\s\S]*?---\s*\n([\s\S]*)$/);
+      if (bodyMatch) {
+        const body = bodyMatch[1];
+        const triggerLines = body.match(/^TRIGGER\s+when:\s*(.+)$/gmi);
+        if (triggerLines) {
+          for (const line of triggerLines) {
+            const m = line.match(/^TRIGGER\s+when:\s*(.+)$/i);
+            if (m) triggers.push(m[1].trim());
+          }
+        }
+      }
+
+      skills.push({
+        name,
+        description,
+        triggers,
+        path: entry.name,
+        file_path: `${entry.name}/SKILL.md`,
+        root: rootInfo.root,
+        scope: rootInfo.scope,
+        installed: rootInfo.scope !== 'import-only',
+        deprecated: !!rootInfo.deprecated,
+      });
+      skillCount++;
+    }
+
+    rootSummary.skill_count = skillCount;
+    roots.push(rootSummary);
   }
 
-  // Sort by name for deterministic output
-  manifest.sort((a, b) => a.name.localeCompare(b.name));
-  return manifest;
+  skills.sort((a, b) => {
+    const rootCmp = a.root.localeCompare(b.root);
+    return rootCmp !== 0 ? rootCmp : a.name.localeCompare(b.name);
+  });
+
+  const gsdSkillsInstalled = skills.some(skill => skill.name.startsWith('gsd-'));
+
+  return {
+    skills,
+    roots,
+    installation: {
+      gsd_skills_installed: gsdSkillsInstalled,
+      legacy_claude_commands_installed: legacyClaudeCommandsInstalled,
+    },
+    counts: {
+      skills: skills.length,
+      roots: roots.length,
+    },
+  };
 }
 
 /**
  * Command: generate skill manifest JSON.
  *
  * Options:
- *   --skills-dir <path>  Path to skills directory (required)
+ *   --skills-dir <path>  Optional absolute path to a single skills directory
  *   --write              Also write to .planning/skill-manifest.json
  */
 function cmdSkillManifest(cwd, args, raw) {
@@ -1667,12 +1799,7 @@ function cmdSkillManifest(cwd, args, raw) {
     ? args[skillsDirIdx + 1]
     : null;
 
-  if (!skillsDir) {
-    output([], raw);
-    return;
-  }
-
-  const manifest = buildSkillManifest(skillsDir);
+  const manifest = buildSkillManifest(cwd, skillsDir);
 
   // Optionally write to .planning/skill-manifest.json
   if (args.includes('--write')) {
diff --git a/get-shit-done/bin/lib/profile-output.cjs b/get-shit-done/bin/lib/profile-output.cjs
index 57040079..38156bac 100644
--- a/get-shit-done/bin/lib/profile-output.cjs
+++ b/get-shit-done/bin/lib/profile-output.cjs
@@ -177,11 +177,11 @@ const CLAUDE_MD_FALLBACKS = {
   stack: 'Technology stack not yet documented. Will populate after codebase mapping or first phase.',
   conventions: 'Conventions not yet established. Will populate as patterns emerge during development.',
   architecture: 'Architecture not yet mapped. Follow existing patterns found in the codebase.',
-  skills: 'No project skills found. Add skills to any of: `.claude/skills/`, `.agents/skills/`, `.cursor/skills/`, or `.github/skills/` with a `SKILL.md` index file.',
+  skills: 'No project skills found. Add skills to any of: `.claude/skills/`, `.agents/skills/`, `.cursor/skills/`, `.github/skills/`, or `.codex/skills/` with a `SKILL.md` index file.',
 };
 
 // Directories where project skills may live (checked in order)
-const SKILL_SEARCH_DIRS = ['.claude/skills', '.agents/skills', '.cursor/skills', '.github/skills'];
+const SKILL_SEARCH_DIRS = ['.claude/skills', '.agents/skills', '.cursor/skills', '.github/skills', '.codex/skills'];
 
 const CLAUDE_MD_WORKFLOW_ENFORCEMENT = [
   'Before using Edit, Write, or other file-changing tools, start work through a GSD command so planning artifacts and execution context stay in sync.',
diff --git a/sdk/src/query/skills.test.ts b/sdk/src/query/skills.test.ts
index af2428c0..ab489fe7 100644
--- a/sdk/src/query/skills.test.ts
+++ b/sdk/src/query/skills.test.ts
@@ -2,29 +2,72 @@
  * Tests for agent skills query handler.
  */
 
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { mkdtemp, mkdir, rm } from 'node:fs/promises';
+import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
+import { mkdtemp, mkdir, rm, writeFile } from 'node:fs/promises';
 import { join } from 'node:path';
 import { tmpdir } from 'node:os';
 
 import { agentSkills } from './skills.js';
 
+function writeSkill(rootDir: string, name: string, description = 'Skill under test') {
+  const skillDir = join(rootDir, name);
+  return mkdir(skillDir, { recursive: true }).then(() => writeFile(join(skillDir, 'SKILL.md'), [
+    '---',
+    `name: ${name}`,
+    `description: ${description}`,
+    '---',
+    '',
+    `# ${name}`,
+  ].join('\n')));
+}
+
 describe('agentSkills', () => {
   let tmpDir: string;
+  let homeDir: string;
 
   beforeEach(async () => {
     tmpDir = await mkdtemp(join(tmpdir(), 'gsd-skills-'));
-    await mkdir(join(tmpDir, '.cursor', 'skills', 'my-skill'), { recursive: true });
+    homeDir = await mkdtemp(join(tmpdir(), 'gsd-skills-home-'));
+    await writeSkill(join(tmpDir, '.cursor', 'skills'), 'my-skill');
+    await writeSkill(join(tmpDir, '.codex', 'skills'), 'project-codex');
+    await mkdir(join(tmpDir, '.claude', 'skills', 'orphaned-dir'), { recursive: true });
+    await writeSkill(join(homeDir, '.claude', 'skills'), 'global-claude');
+    await writeSkill(join(homeDir, '.codex', 'skills'), 'global-codex');
+    await writeSkill(join(homeDir, '.claude', 'get-shit-done', 'skills'), 'legacy-import');
+    vi.stubEnv('HOME', homeDir);
   });
 
   afterEach(async () => {
+    vi.unstubAllEnvs();
     await rm(tmpDir, { recursive: true, force: true });
+    await rm(homeDir, { recursive: true, force: true });
   });
 
-  it('returns deduped skill names from project skill dirs', async () => {
+  it('returns deduped skill names from project and managed global skill dirs', async () => {
     const r = await agentSkills(['gsd-executor'], tmpDir);
     const data = r.data as Record<string, unknown>;
-    expect(data.skill_count).toBeGreaterThan(0);
-    expect((data.skills as string[]).length).toBeGreaterThan(0);
+    const skills = data.skills as string[];
+
+    expect(skills).toEqual(expect.arrayContaining([
+      'my-skill',
+      'project-codex',
+      'global-claude',
+      'global-codex',
+    ]));
+    expect(skills).not.toContain('orphaned-dir');
+    expect(skills).not.toContain('legacy-import');
+    expect(data.skill_count).toBe(skills.length);
+  });
+
+  it('counts deduped skill names when the same skill exists in multiple roots', async () => {
+    await writeSkill(join(tmpDir, '.claude', 'skills'), 'shared-skill');
+    await writeSkill(join(tmpDir, '.agents', 'skills'), 'shared-skill');
+
+    const r = await agentSkills(['gsd-executor'], tmpDir);
+    const data = r.data as Record<string, unknown>;
+    const skills = data.skills as string[];
+
+    expect(skills.filter((skill) => skill === 'shared-skill')).toHaveLength(1);
+    expect(data.skill_count).toBe(skills.length);
   });
 });
diff --git a/sdk/src/query/skills.ts b/sdk/src/query/skills.ts
index 7e3a4667..870ea756 100644
--- a/sdk/src/query/skills.ts
+++ b/sdk/src/query/skills.ts
@@ -1,8 +1,9 @@
 /**
  * Agent skills query handler — scan installed skill directories.
  *
- * Reads from .claude/skills/, .agents/skills/, .cursor/skills/, .github/skills/,
- * and the global ~/.claude/get-shit-done/skills/ directory.
+ * Reads from project `.claude/skills/`, `.agents/skills/`, `.cursor/skills/`,
+ * `.github/skills/`, `.codex/skills/`, plus managed global `~/.claude/skills/`
+ * and `~/.codex/skills/` roots.
  *
  * @example
  * ```typescript
@@ -26,7 +27,9 @@ export const agentSkills: QueryHandler = async (args, projectDir) => {
     join(projectDir, '.agents', 'skills'),
     join(projectDir, '.cursor', 'skills'),
     join(projectDir, '.github', 'skills'),
-    join(homedir(), '.claude', 'get-shit-done', 'skills'),
+    join(projectDir, '.codex', 'skills'),
+    join(homedir(), '.claude', 'skills'),
+    join(homedir(), '.codex', 'skills'),
   ];
 
   const skills: string[] = [];
@@ -35,16 +38,19 @@ export const agentSkills: QueryHandler = async (args, projectDir) => {
     try {
       const entries = readdirSync(dir, { withFileTypes: true });
       for (const entry of entries) {
-        if (entry.isDirectory()) skills.push(entry.name);
+        if (!entry.isDirectory()) continue;
+        if (!existsSync(join(dir, entry.name, 'SKILL.md'))) continue;
+        skills.push(entry.name);
       }
     } catch { /* skip */ }
   }
 
+  const dedupedSkills = [...new Set(skills)];
   return {
     data: {
       agent_type: agentType,
-      skills: [...new Set(skills)],
-      skill_count: skills.length,
+      skills: dedupedSkills,
+      skill_count: dedupedSkills.length,
     },
   };
 };
diff --git a/tests/claude-md.test.cjs b/tests/claude-md.test.cjs
index 3ac0f1c3..cd7b3a04 100644
--- a/tests/claude-md.test.cjs
+++ b/tests/claude-md.test.cjs
@@ -148,6 +148,38 @@ describe('generate-claude-md skills section', () => {
     assert.ok(content.includes('ERP synchronization flows'));
   });
 
+  test('discovers skills from .codex/skills/ directory and ignores deprecated import-only roots', () => {
+    const codexSkillDir = path.join(tmpDir, '.codex', 'skills', 'automation');
+    fs.mkdirSync(codexSkillDir, { recursive: true });
+    fs.writeFileSync(
+      path.join(codexSkillDir, 'SKILL.md'),
+      '---\nname: automation\ndescription: Project Codex skill.\n---\n\n# Automation\n'
+    );
+
+    const homeDir = fs.mkdtempSync(path.join(require('os').tmpdir(), 'gsd-claude-skills-home-'));
+    fs.mkdirSync(path.join(homeDir, '.claude', 'get-shit-done', 'skills', 'import-only'), { recursive: true });
+    fs.writeFileSync(
+      path.join(homeDir, '.claude', 'get-shit-done', 'skills', 'import-only', 'SKILL.md'),
+      '---\nname: import-only\ndescription: Deprecated import-only skill.\n---\n'
+    );
+
+    const originalHome = process.env.HOME;
+    process.env.HOME = homeDir;
+
+    try {
+      const result = runGsdTools('generate-claude-md', tmpDir);
+      assert.ok(result.success, `Command failed: ${result.error}`);
+
+      const content = fs.readFileSync(path.join(tmpDir, 'CLAUDE.md'), 'utf-8');
+      assert.ok(content.includes('automation'));
+      assert.ok(content.includes('Project Codex skill'));
+      assert.ok(!content.includes('import-only'));
+    } finally {
+      process.env.HOME = originalHome;
+      cleanup(homeDir);
+    }
+  });
+
   test('skips gsd- prefixed skill directories', () => {
     const gsdSkillDir = path.join(tmpDir, '.claude', 'skills', 'gsd-plan-phase');
     const userSkillDir = path.join(tmpDir, '.claude', 'skills', 'my-feature');
diff --git a/tests/profile-output.test.cjs b/tests/profile-output.test.cjs
index 160ab71b..05364b1a 100644
--- a/tests/profile-output.test.cjs
+++ b/tests/profile-output.test.cjs
@@ -157,6 +157,19 @@ describe('generate-claude-md command', () => {
     const content = fs.readFileSync(outputPath, 'utf-8');
     assert.ok(content.length > 0, 'should still have content');
   });
+
+  test('skills fallback mentions the normalized project roots', () => {
+    const result = runGsdTools('generate-claude-md', tmpDir);
+    assert.ok(result.success, `Failed: ${result.error}`);
+
+    const content = fs.readFileSync(path.join(tmpDir, 'CLAUDE.md'), 'utf-8');
+    assert.ok(content.includes('.claude/skills/'));
+    assert.ok(content.includes('.agents/skills/'));
+    assert.ok(content.includes('.cursor/skills/'));
+    assert.ok(content.includes('.github/skills/'));
+    assert.ok(content.includes('.codex/skills/'));
+    assert.ok(!content.includes('get-shit-done/skills'));
+  });
 });
 
 // ─── generate-dev-preferences ─────────────────────────────────────────────────
diff --git a/tests/skill-manifest.test.cjs b/tests/skill-manifest.test.cjs
index cb18110a..77ec7e55 100644
--- a/tests/skill-manifest.test.cjs
+++ b/tests/skill-manifest.test.cjs
@@ -1,6 +1,5 @@
 /**
  * Tests for skill-manifest command
- * TDD: RED phase — tests written before implementation
  */
 
 const { describe, test, beforeEach, afterEach } = require('node:test');
@@ -9,211 +8,123 @@ const fs = require('fs');
 const path = require('path');
 const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
 
+function writeSkill(rootDir, name, description, body = '') {
+  const skillDir = path.join(rootDir, name);
+  fs.mkdirSync(skillDir, { recursive: true });
+  fs.writeFileSync(path.join(skillDir, 'SKILL.md'), [
+    '---',
+    `name: ${name}`,
+    `description: ${description}`,
+    '---',
+    '',
+    body || `# ${name}`,
+  ].join('\n'));
+}
+
 describe('skill-manifest', () => {
   let tmpDir;
+  let homeDir;
 
   beforeEach(() => {
     tmpDir = createTempProject();
+    homeDir = fs.mkdtempSync(path.join(require('os').tmpdir(), 'gsd-skill-manifest-home-'));
+
+    writeSkill(path.join(tmpDir, '.claude', 'skills'), 'project-claude', 'Project Claude skill');
+    writeSkill(path.join(tmpDir, '.claude', 'skills'), 'gsd-help', 'Installed GSD skill');
+    writeSkill(path.join(tmpDir, '.agents', 'skills'), 'project-agents', 'Project agent skill');
+    writeSkill(path.join(tmpDir, '.codex', 'skills'), 'project-codex', 'Project Codex skill');
+
+    writeSkill(path.join(homeDir, '.claude', 'skills'), 'global-claude', 'Global Claude skill');
+    writeSkill(path.join(homeDir, '.codex', 'skills'), 'global-codex', 'Global Codex skill');
+    writeSkill(
+      path.join(homeDir, '.claude', 'get-shit-done', 'skills'),
+      'legacy-import',
+      'Deprecated import-only skill'
+    );
+
+    fs.mkdirSync(path.join(homeDir, '.claude', 'commands', 'gsd'), { recursive: true });
+    fs.writeFileSync(path.join(homeDir, '.claude', 'commands', 'gsd', 'help.md'), '# legacy');
   });
 
   afterEach(() => {
     cleanup(tmpDir);
+    cleanup(homeDir);
   });
 
-  test('skill-manifest command exists and returns JSON', () => {
-    // Create a skills directory with one skill
-    const skillDir = path.join(tmpDir, '.claude', 'skills', 'test-skill');
-    fs.mkdirSync(skillDir, { recursive: true });
-    fs.writeFileSync(path.join(skillDir, 'SKILL.md'), [
-      '---',
-      'name: test-skill',
-      'description: A test skill',
-      '---',
-      '',
-      '# Test Skill',
-    ].join('\n'));
-
-    const result = runGsdTools(['skill-manifest', '--skills-dir', path.join(tmpDir, '.claude', 'skills')], tmpDir);
+  test('returns normalized inventory across canonical roots', () => {
+    const result = runGsdTools(['skill-manifest'], tmpDir, { HOME: homeDir });
     assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
 
     const manifest = JSON.parse(result.output);
-    assert.ok(Array.isArray(manifest), 'Manifest should be an array');
-  });
+    assert.ok(Array.isArray(manifest.skills), 'skills should be an array');
+    assert.ok(Array.isArray(manifest.roots), 'roots should be an array');
+    assert.ok(manifest.installation && typeof manifest.installation === 'object', 'installation summary present');
+    assert.ok(manifest.counts && typeof manifest.counts === 'object', 'counts summary present');
 
-  test('generates manifest with correct structure from SKILL.md frontmatter', () => {
-    const skillDir = path.join(tmpDir, '.claude', 'skills', 'my-skill');
-    fs.mkdirSync(skillDir, { recursive: true });
-    fs.writeFileSync(path.join(skillDir, 'SKILL.md'), [
-      '---',
-      'name: my-skill',
-      'description: Does something useful',
-      '---',
-      '',
-      '# My Skill',
-      '',
-      'TRIGGER when: user asks about widgets',
-    ].join('\n'));
+    const skillNames = manifest.skills.map((skill) => skill.name).sort();
+    assert.deepStrictEqual(skillNames, [
+      'global-claude',
+      'global-codex',
+      'gsd-help',
+      'legacy-import',
+      'project-agents',
+      'project-claude',
+      'project-codex',
+    ]);
 
-    const result = runGsdTools(['skill-manifest', '--skills-dir', path.join(tmpDir, '.claude', 'skills')], tmpDir);
-    assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
+    const codexSkill = manifest.skills.find((skill) => skill.name === 'project-codex');
+    assert.deepStrictEqual(
+      {
+        root: codexSkill.root,
+        scope: codexSkill.scope,
+        installed: codexSkill.installed,
+        deprecated: codexSkill.deprecated,
+      },
+      {
+        root: '.codex/skills',
+        scope: 'project',
+        installed: true,
+        deprecated: false,
+      }
+    );
 
-    const manifest = JSON.parse(result.output);
-    assert.strictEqual(manifest.length, 1);
-    assert.strictEqual(manifest[0].name, 'my-skill');
-    assert.strictEqual(manifest[0].description, 'Does something useful');
-    assert.strictEqual(manifest[0].path, 'my-skill');
-  });
+    const importedSkill = manifest.skills.find((skill) => skill.name === 'legacy-import');
+    assert.deepStrictEqual(
+      {
+        root: importedSkill.root,
+        scope: importedSkill.scope,
+        installed: importedSkill.installed,
+        deprecated: importedSkill.deprecated,
+      },
+      {
+        root: '~/.claude/get-shit-done/skills',
+        scope: 'import-only',
+        installed: false,
+        deprecated: true,
+      }
+    );
 
-  test('empty skills directory produces empty manifest', () => {
-    const skillsDir = path.join(tmpDir, '.claude', 'skills');
-    fs.mkdirSync(skillsDir, { recursive: true });
+    const gsdSkill = manifest.skills.find((skill) => skill.name === 'gsd-help');
+    assert.strictEqual(gsdSkill.installed, true);
 
-    const result = runGsdTools(['skill-manifest', '--skills-dir', skillsDir], tmpDir);
-    assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
+    const legacyRoot = manifest.roots.find((root) => root.scope === 'legacy-commands');
+    assert.ok(legacyRoot, 'legacy commands root should be reported');
+    assert.strictEqual(legacyRoot.present, true);
 
-    const manifest = JSON.parse(result.output);
-    assert.ok(Array.isArray(manifest), 'Manifest should be an array');
-    assert.strictEqual(manifest.length, 0);
-  });
-
-  test('skills without SKILL.md are skipped', () => {
-    const skillsDir = path.join(tmpDir, '.claude', 'skills');
-    // Skill with SKILL.md
-    const goodDir = path.join(skillsDir, 'good-skill');
-    fs.mkdirSync(goodDir, { recursive: true });
-    fs.writeFileSync(path.join(goodDir, 'SKILL.md'), [
-      '---',
-      'name: good-skill',
-      'description: Has a SKILL.md',
-      '---',
-      '',
-      '# Good Skill',
-    ].join('\n'));
-
-    // Skill without SKILL.md (just a directory)
-    const badDir = path.join(skillsDir, 'bad-skill');
-    fs.mkdirSync(badDir, { recursive: true });
-    fs.writeFileSync(path.join(badDir, 'README.md'), '# No SKILL.md here');
-
-    const result = runGsdTools(['skill-manifest', '--skills-dir', skillsDir], tmpDir);
-    assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
-
-    const manifest = JSON.parse(result.output);
-    assert.strictEqual(manifest.length, 1);
-    assert.strictEqual(manifest[0].name, 'good-skill');
-  });
-
-  test('manifest includes frontmatter fields from SKILL.md', () => {
-    const skillDir = path.join(tmpDir, '.claude', 'skills', 'rich-skill');
-    fs.mkdirSync(skillDir, { recursive: true });
-    fs.writeFileSync(path.join(skillDir, 'SKILL.md'), [
-      '---',
-      'name: rich-skill',
-      'description: A richly documented skill',
-      '---',
-      '',
-      '# Rich Skill',
-      '',
-      'TRIGGER when: user mentions databases',
-      'DO NOT TRIGGER when: user asks about frontend',
-    ].join('\n'));
-
-    const result = runGsdTools(['skill-manifest', '--skills-dir', path.join(tmpDir, '.claude', 'skills')], tmpDir);
-    assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
-
-    const manifest = JSON.parse(result.output);
-    assert.strictEqual(manifest.length, 1);
-
-    const skill = manifest[0];
-    assert.strictEqual(skill.name, 'rich-skill');
-    assert.strictEqual(skill.description, 'A richly documented skill');
-    assert.strictEqual(skill.path, 'rich-skill');
-    // triggers extracted from body text
-    assert.ok(Array.isArray(skill.triggers), 'triggers should be an array');
-    assert.ok(skill.triggers.length > 0, 'triggers should have at least one entry');
-    assert.ok(skill.triggers.some(t => t.includes('databases')), 'triggers should mention databases');
-  });
-
-  test('multiple skills are all included in manifest', () => {
-    const skillsDir = path.join(tmpDir, '.claude', 'skills');
-
-    for (const name of ['alpha', 'beta', 'gamma']) {
-      const dir = path.join(skillsDir, name);
-      fs.mkdirSync(dir, { recursive: true });
-      fs.writeFileSync(path.join(dir, 'SKILL.md'), [
-        '---',
-        `name: ${name}`,
-        `description: The ${name} skill`,
-        '---',
-        '',
-        `# ${name}`,
-      ].join('\n'));
-    }
-
-    const result = runGsdTools(['skill-manifest', '--skills-dir', skillsDir], tmpDir);
-    assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
-
-    const manifest = JSON.parse(result.output);
-    assert.strictEqual(manifest.length, 3);
-    const names = manifest.map(s => s.name).sort();
-    assert.deepStrictEqual(names, ['alpha', 'beta', 'gamma']);
+    assert.strictEqual(manifest.installation.gsd_skills_installed, true);
+    assert.strictEqual(manifest.installation.legacy_claude_commands_installed, true);
+    assert.strictEqual(manifest.counts.skills, 7);
   });
 
   test('writes manifest to .planning/skill-manifest.json when --write flag is used', () => {
-    const skillDir = path.join(tmpDir, '.claude', 'skills', 'write-test');
-    fs.mkdirSync(skillDir, { recursive: true });
-    fs.writeFileSync(path.join(skillDir, 'SKILL.md'), [
-      '---',
-      'name: write-test',
-      'description: Tests write mode',
-      '---',
-      '',
-      '# Write Test',
-    ].join('\n'));
-
-    const result = runGsdTools(['skill-manifest', '--skills-dir', path.join(tmpDir, '.claude', 'skills'), '--write'], tmpDir);
+    const result = runGsdTools(['skill-manifest', '--write'], tmpDir, { HOME: homeDir });
     assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
 
     const manifestPath = path.join(tmpDir, '.planning', 'skill-manifest.json');
     assert.ok(fs.existsSync(manifestPath), 'skill-manifest.json should be written to .planning/');
 
     const manifest = JSON.parse(fs.readFileSync(manifestPath, 'utf-8'));
-    assert.strictEqual(manifest.length, 1);
-    assert.strictEqual(manifest[0].name, 'write-test');
-  });
-
-  test('nonexistent skills directory returns empty manifest', () => {
-    const result = runGsdTools(['skill-manifest', '--skills-dir', path.join(tmpDir, 'nonexistent')], tmpDir);
-    assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
-
-    const manifest = JSON.parse(result.output);
-    assert.ok(Array.isArray(manifest), 'Manifest should be an array');
-    assert.strictEqual(manifest.length, 0);
-  });
-
-  test('files in skills directory are ignored (only subdirectories scanned)', () => {
-    const skillsDir = path.join(tmpDir, '.claude', 'skills');
-    fs.mkdirSync(skillsDir, { recursive: true });
-    // A file, not a directory
-    fs.writeFileSync(path.join(skillsDir, 'not-a-skill.md'), '# Not a skill');
-
-    // A valid skill directory
-    const skillDir = path.join(skillsDir, 'real-skill');
-    fs.mkdirSync(skillDir, { recursive: true });
-    fs.writeFileSync(path.join(skillDir, 'SKILL.md'), [
-      '---',
-      'name: real-skill',
-      'description: A real skill',
-      '---',
-      '',
-      '# Real Skill',
-    ].join('\n'));
-
-    const result = runGsdTools(['skill-manifest', '--skills-dir', skillsDir], tmpDir);
-    assert.ok(result.success, `Command should succeed: ${result.error || result.output}`);
-
-    const manifest = JSON.parse(result.output);
-    assert.strictEqual(manifest.length, 1);
-    assert.strictEqual(manifest[0].name, 'real-skill');
+    assert.ok(Array.isArray(manifest.skills));
+    assert.ok(manifest.installation);
   });
 });