repo-root/
├── .agents/
│   ├── AGENTS.md                                           # Canonical agent instructions
│   └── skills/<name>/SKILL.md                              # Canonical skill source
├── AGENTS.md → .agents/AGENTS.md                           # Symlink (tools reading repo root)
├── CLAUDE.md → .agents/AGENTS.md                           # Symlink (Claude reads repo root)
├── .codex/AGENTS.md → ../.agents/AGENTS.md                 # Symlink
├── .gemini/GEMINI.md → ../.agents/AGENTS.md                # Symlink
├── .claude/skills/<name> → ../../.agents/skills/<name>     # Per-skill symlink
├── .codex/skills/<name> → ../../.agents/skills/<name>      # Per-skill symlink
├── .codex-home/skills/<name> → ../../.agents/skills/<name> # Per-skill symlink
└── .gitignore                                              # Whitelist entries for all paths

Key rules:

.agents/ is the single source of truth for both agent instructions and skills
.agents/AGENTS.md is the canonical agent instruction file — all tool-specific files are symlinks
Per-skill symlinks are used instead of directory-level symlinks so externally installed skills (e.g. via npx skills add) coexist without conflict
.gitignore uses a base skills/ ignore rule, then whitelists specific paths
An optional evals/ directory inside .agents/skills/<name>/ is always gitignored
No skill may live as a real directory under a tool-specific path (.claude/skills/<name>/, .codex/skills/<name>/, .codex-home/skills/<name>/). Per-tool dirs contain only symlinks. Canonical source is always .agents/skills/<name>/ — this keeps skills cross-tool and prevents silent Claude-only (or Codex-only, etc.) drift

Phase 1: Gather Context

Before asking questions, run discovery:

ls .agents/ 2>/dev/null
ls .agents/skills/ 2>/dev/null
ls .claude/commands/ 2>/dev/null
cat CLAUDE.md 2>/dev/null | head -5
cat AGENTS.md 2>/dev/null | head -5
grep -n "^skills/" .gitignore 2>/dev/null

Also run the cross-tool audit (see Audit commands for the copy-paste block). Detect:

Tool-specific real-dir skills — any directory under .claude/skills/, .codex/skills/, or .codex-home/skills/ that is a real directory (not a symlink). These violate the cross-tool rule and must be promoted.
Orphans in .agents/skills/ — any skill in .agents/skills/ that is missing a symlink in one or more per-tool dirs. These are reachable from some tools but not others.

Present all findings (shared-context reads + audit output), then use AskUserQuestion with these questions (max 4 per call):

Mode: "Do you want to (a) create a NEW repo-local skill from scratch, (b) refactor an existing .claude/commands/ file into the cross-tool skill structure, (c) just set up agent instructions (no skill), (d) promote an existing tool-specific real-dir skill into the cross-tool layout, or (e) repair an orphan .agents/skills/ skill by creating missing per-tool symlinks?"
Skill name (if a/b/d/e): "What should the skill be called? (kebab-case, e.g. grove-api-review)"
Description (if a or b): "One-line description of what the skill does."
If commands exist and mode = b: "Which command file should I migrate?" (list the files found in .claude/commands/)

If the audit surfaced violations or orphans, lead with those — it's almost always the right next action before scaffolding anything new.

Phase 2a: Agent Instructions

Set up .agents/AGENTS.md as the canonical agent instruction file with symlinks for every tool.

Step 1 — Create or migrate the canonical file:

mkdir -p .agents

If AGENTS.md exists at repo root and is a regular file, move it: mv AGENTS.md .agents/AGENTS.md
If CLAUDE.md exists at repo root and is a regular file (not a symlink), move it: mv CLAUDE.md .agents/AGENTS.md
If neither exists, create .agents/AGENTS.md with a minimal skeleton
If both exist, merge them into .agents/AGENTS.md (prefer AGENTS.md content, append unique CLAUDE.md content)

Step 2 — Create symlinks:

ln -sf .agents/AGENTS.md AGENTS.md
ln -sf .agents/AGENTS.md CLAUDE.md
mkdir -p .codex .gemini
ln -sf ../.agents/AGENTS.md .codex/AGENTS.md
ln -sf ../.agents/AGENTS.md .gemini/GEMINI.md

Step 3 — Verify all symlinks resolve:

readlink AGENTS.md
readlink CLAUDE.md
readlink .codex/AGENTS.md
readlink .gemini/GEMINI.md
head -3 CLAUDE.md

Step 4 — Update .gitignore:

Check if entries already exist, then add as needed:

grep -n "AGENTS.md\|CLAUDE.md\|GEMINI.md" .gitignore 2>/dev/null

Append the agent instructions block from the gitignore template if not present.

Phase 2b: Scaffold, Promote, or Repair the Skill

Skip this phase if the user chose mode (c) in Phase 1. Modes (a), (b), (d), and (e) all share the same symlink + gitignore steps — they only differ in how the canonical source is produced.

Create canonical source

Create the canonical directory:

mkdir -p .agents/skills/<name>

If creating new (mode a):

Create .agents/skills/<name>/SKILL.md with frontmatter and a minimal skeleton. Ask the user to provide or iterate on the skill content.

If refactoring from .claude/commands/ (mode b):

Read the source command file (e.g., .claude/commands/<name>.md)
Create .agents/skills/<name>/SKILL.md with YAML frontmatter added
Convert the top-level header to include 
Do NOT delete the original command file yet — offer in Phase 3

If promoting an existing tool-specific real-dir skill (mode d):

The skill currently lives as a real directory under a per-tool path (e.g., .claude/skills/<name>/ with a real SKILL.md inside). Move it to the canonical location:

mv .claude/skills/<name> .agents/skills/<name>

If the violation is under .codex/skills/ or .codex-home/skills/ instead, mv from there. Then proceed to Create symlinks — a symlink must be re-added to the per-tool dir the skill was promoted from (since the mv removed it), and to the other two per-tool dirs.

If repairing an orphan (mode e):

The skill already lives at .agents/skills/<name>/ but is missing one or more per-tool symlinks. Skip directly to Create symlinks — the canonical source is untouched; only the symlinks need to be (re-)created.

Create symlinks

Each skill needs a symlink in every tool's skills directory. This approach allows external skills (e.g. from npx skills add) to coexist.

mkdir -p .claude/skills .codex/skills .codex-home/skills
ln -sf ../../.agents/skills/<name> .claude/skills/<name>
ln -sf ../../.agents/skills/<name> .codex/skills/<name>
ln -sf ../../.agents/skills/<name> .codex-home/skills/<name>

Check that the symlinks resolve correctly:

test -f .claude/skills/<name>/SKILL.md && echo "OK" || echo "BROKEN"

Two legacy layouts require normalization before this loop runs cleanly:

Legacy — directory-level symlink (.claude/skills → ../.agents/skills). Replace with per-skill symlinks:

for tool in .claude .codex .codex-home; do
  [ -L "$tool/skills" ] && rm "$tool/skills"
  mkdir -p "$tool/skills"
done

Legacy — tool-specific real-dir skill (a real .claude/skills/<name>/ or .codex/skills/<name>/ dir, not a symlink). Promote to canonical first:

for tool in .claude .codex .codex-home; do
  for d in "$tool"/skills/*/; do
    [ -d "$d" ] && [ ! -L "${d%/}" ] || continue
    name=$(basename "${d%/}")
    # Skip if a canonical source already exists (manual conflict resolution needed)
    [ -d ".agents/skills/$name" ] && { echo "CONFLICT: .agents/skills/$name already exists; resolve manually"; continue; }
    mv "${d%/}" ".agents/skills/$name"
  done
done

After either normalization, populate all three per-tool dirs with per-skill symlinks:

mkdir -p .claude/skills .codex/skills .codex-home/skills
for skill in .agents/skills/*/; do
  name=$(basename "$skill")
  ln -sf "../../.agents/skills/$name" ".claude/skills/$name"
  ln -sf "../../.agents/skills/$name" ".codex/skills/$name"
  ln -sf "../../.agents/skills/$name" ".codex-home/skills/$name"
done

ln -sf makes this idempotent — safe to re-run on a partially-configured repo (mode e).

Update .gitignore

The gitignore must be updated carefully to preserve existing entries.

Step 1 — Check if the base skills/ rule exists:

grep -n "^skills/" .gitignore

Step 2 — Check if entries for this skill already exist:

grep "<name>" .gitignore

Step 3 — Append or insert the whitelist block.

If NO skills/ section exists, append the full block from the gitignore template.

If a skills/ section already exists (adding a 2nd+ skill), only add the NEW skill-specific lines. The base rules (skills/, !.agents/skills/, !.claude/skills, !.codex/skills, !.codex-home/skills) already exist — do NOT duplicate them. Insert the new lines after the last entry:

!.agents/skills/<name>/
!.agents/skills/<name>/SKILL.md
.agents/skills/<name>/evals/

Never duplicate a line that already exists in .gitignore.

Phase 3: Verify

Run these checks and report results:

# Verify agent instruction symlinks
readlink AGENTS.md
readlink CLAUDE.md
readlink .codex/AGENTS.md
readlink .gemini/GEMINI.md
head -1 CLAUDE.md

If skills were scaffolded, promoted, or repaired:

# Verify per-skill symlinks resolve correctly
readlink .claude/skills/<name>
readlink .codex/skills/<name>
readlink .codex-home/skills/<name>

# Verify skill content is accessible through each symlink
head -3 .claude/skills/<name>/SKILL.md
head -3 .codex/skills/<name>/SKILL.md
head -3 .codex-home/skills/<name>/SKILL.md

# Verify git tracks the canonical skill file
git status .agents/skills/<name>/SKILL.md

# Lint: all three per-tool symlink entries must be whitelisted in .gitignore
for tool in .claude .codex .codex-home; do
  grep -q "^!$tool/skills/<name>$" .gitignore \
    || echo "FAIL: .gitignore missing '!$tool/skills/<name>'"
done

# Lint: no real-dir skills should remain under any per-tool path
for tool in .claude .codex .codex-home; do
  find "$tool/skills" -mindepth 1 -maxdepth 1 -type d -not -name skills \
    | while read d; do echo "FAIL: real-dir skill at $d (should be a symlink)"; done
done

If refactoring, ask: "The original command file at .claude/commands/<file> still exists. Should I delete it now that the skill has been migrated?"

Present summary:

Agent instructions:
  Canonical: .agents/AGENTS.md
  AGENTS.md → .agents/AGENTS.md                → ✅
  CLAUDE.md → .agents/AGENTS.md                → ✅
  .codex/AGENTS.md → ../.agents/AGENTS.md      → ✅
  .gemini/GEMINI.md → ../.agents/AGENTS.md     → ✅

Skill: <name>
  Canonical: .agents/skills/<name>/SKILL.md
  .claude/skills/<name> → ../../.agents/skills/<name>      → ✅
  .codex/skills/<name> → ../../.agents/skills/<name>       → ✅
  .codex-home/skills/<name> → ../../.agents/skills/<name>  → ✅

Gitignore: ✅ updated

Templates

SKILL.md frontmatter template

 ---
 name: <skill-name>
 description: <one-line description>
 disable-model-invocation: false
 ---

 # Skill Title <!-- omit in toc -->

AGENTS.md skeleton template

# AGENTS.md <!-- omit in toc -->

## Project Overview

- Brief description of the project

## Development

- Key commands and workflows

Gitignore block template

Full block for agent instructions (add once per repo):

# Agent instructions
# Canonical source: .agents/AGENTS.md — tool-specific files are symlinks
!.agents/
!.agents/AGENTS.md

Full block for the first skill in a repo (replace <name> with the skill name):

# Skills
# Default: ignore generic skills/ trees from external skill repos.
# Exception: keep repo-local cross-tool skills tracked via per-skill symlinks.
skills/
!.agents/skills/
!.agents/skills/<name>/
!.agents/skills/<name>/SKILL.md
.agents/skills/<name>/evals/
# Per-skill symlinks — track each symlink so all tools discover the skill
!.claude/skills/
!.claude/skills/<name>
!.codex/skills/
!.codex/skills/<name>
!.codex-home/skills/
!.codex-home/skills/<name>

For additional skills, append only the new skill-specific lines:

!.agents/skills/<name>/
!.agents/skills/<name>/SKILL.md
.agents/skills/<name>/evals/
!.claude/skills/<name>
!.codex/skills/<name>
!.codex-home/skills/<name>

Audit commands

Use these during Phase 1 to surface cross-tool drift before scaffolding anything new.

Detect tool-specific real-dir skills (violations — a skill that exists under a per-tool path as a real directory, not a symlink):

for tool in .claude .codex .codex-home; do
  [ -d "$tool/skills" ] || continue
  find "$tool/skills" -mindepth 1 -maxdepth 1 -type d -not -name skills 2>/dev/null \
    | while read d; do echo "VIOLATION: real-dir skill at $d"; done
done

Detect orphans (skill exists in .agents/skills/ but is missing a symlink in one or more per-tool dirs):

[ -d .agents/skills ] && for skill in .agents/skills/*/; do
  name=$(basename "${skill%/}")
  for tool in .claude .codex .codex-home; do
    [ -L "$tool/skills/$name" ] || echo "ORPHAN: .agents/skills/$name missing $tool/skills/$name"
  done
done

Detect broken symlinks (target missing):

for tool in .claude .codex .codex-home; do
  [ -d "$tool/skills" ] || continue
  find "$tool/skills" -maxdepth 1 -type l -exec test ! -e {} \; -print \
    | while read l; do echo "BROKEN: $l"; done
done

Empty output from all three = healthy cross-tool layout.

Symlink commands template

Agent instructions setup (run once per repo):

mkdir -p .agents .codex .gemini
ln -sf .agents/AGENTS.md AGENTS.md
ln -sf .agents/AGENTS.md CLAUDE.md
ln -sf ../.agents/AGENTS.md .codex/AGENTS.md
ln -sf ../.agents/AGENTS.md .gemini/GEMINI.md

Per-skill setup (run for each new skill):

mkdir -p .agents/skills/<name> .claude/skills .codex/skills .codex-home/skills
ln -sf ../../.agents/skills/<name> .claude/skills/<name>
ln -sf ../../.agents/skills/<name> .codex/skills/<name>
ln -sf ../../.agents/skills/<name> .codex-home/skills/<name>

cmd-skills-local-repo

Repo-Local Skill Manager

Architecture