apply-agent-rules

Install agent rules into a target project, preserving directory structure. Works like npx skills: any git repo is a valid source.

What is this? (read me first)

First, a feature of AI coding agents that a lot of people don't know about. Most folks assume an agent reads a single rules file at the repo root (one CLAUDE.md, one AGENTS.md) and that's it. But agents like Claude Code, Codex, and Cursor also read rules files inside subdirectories — and a rules file in a folder only applies while the agent is working in that folder.

That means you can put a CLAUDE.md in app/Models/ with rules just for models, another in database/migrations/ with rules just for migrations, and so on. Localized rules, sitting right next to the code they govern, automatically picked up when the agent touches that part of the tree. It's a powerful feature, and it's the whole reason this tool exists.

The catch: those per-directory files are valuable but painful to share. Each agent reads a different filename (Claude Code → CLAUDE.md, Codex/others → AGENTS.md, Cursor → .cursorrules, Windsurf → .windsurfrules…), so if you want the same conventions across many repos you end up hand-copying a whole tree of files, under every agent's name, in every project. They drift instantly.

apply-agent-rules fixes that. You keep one rules repo whose directory layout mirrors a real project, then install it into any project. The tool walks the whole tree and drops each rule file at the same relative path, rendered to whichever agents that project uses. update later re-pulls without clobbering edits you've made locally. Think npx-style installer, but for a directory tree of agent rules.

Simplest possible example

You have a rules repo leek/laravel-agent-rules. Its layout mirrors a Laravel project, with a rule file per directory:

CLAUDE.md                       ← project-wide rules
app/Models/CLAUDE.md            ← rules that apply only under app/Models
database/migrations/CLAUDE.md   ← rules that apply only to migrations

From inside any project, run:

npx apply-agent-rules apply leek/laravel-agent-rules --agents claude,cursor

The tool reproduces that entire tree in your project, and because you picked two agents, each rule file lands under both agents' filenames at its original path:

CLAUDE.md                       .cursorrules
app/Models/CLAUDE.md            app/Models/.cursorrules
database/migrations/CLAUDE.md   database/migrations/.cursorrules

So your app/Models rules end up exactly where Claude Code and Cursor look for localized guidance — not flattened into one giant root file. Later, npx apply-agent-rules update re-pulls and refreshes the whole tree; anything you hand-edited locally is detected and left alone. That's the whole idea — the sections below are just the details.

How the source repo is structured

Source repos keep a single canonical rule file per directory — either CLAUDE.md or AGENTS.md. At install time you pick which agents you want (claude, codex, gemini, cursor, windsurf, cline), and that one source file is rendered to each selected agent's expected filename in the same directory. No need to duplicate the same content under six names in your rules repo.

Quick start

# Preview a source repo without writing anything
npx apply-agent-rules list leek/laravel-agent-rules --agents claude,codex

# Pick agents interactively, install into the current directory
npx apply-agent-rules apply leek/laravel-agent-rules

# Or pass agents non-interactively
npx apply-agent-rules apply leek/laravel-agent-rules --agents claude,codex

# Re-pull from the recorded source (preserves local edits, prunes deletes)
npx apply-agent-rules update

How it works

1. Resolves the source: GitHub shorthand and git URLs are cloned shallowly into a temp dir; local paths are used directly.
2. Walks the source tree.
3. For each canonical rule file (basename CLAUDE.md or AGENTS.md), writes a copy at the same relative directory under each selected agent's expected filename.
4. All other files — assets, configs, even files literally named GEMINI.md or .cursorrules in the source — are copied verbatim with no renaming.
5. Existing files are skipped by default — re-running is safe. Use --force to overwrite.
6. Writes .apply-agent-rules.lock.json recording source, ref, commit, agents, and a SHA-256 for every installed file. update uses this to detect local edits and prune deletes.

Example. Source repo (author chose CLAUDE.md as their canonical name):

database/seeders/CLAUDE.md
app/Models/CLAUDE.md
app/Models/notes.txt

apply leek/repo --agents codex --target ./my-app produces:

my-app/database/seeders/AGENTS.md      (rendered from CLAUDE.md)
my-app/app/Models/AGENTS.md            (rendered from CLAUDE.md)
my-app/app/Models/notes.txt            (copied as-is)
my-app/.apply-agent-rules.lock.json

No CLAUDE.md files are written because the user only picked codex.

If two canonical rule files live in the same directory (CLAUDE.md and AGENTS.md side by side), AGENTS.md wins for any target filename you don't have a literal match for, and a warning prints. Pick one canonical name per directory.

Agents

id	canonical filename	scope dir
claude	CLAUDE.md	.claude/
codex	AGENTS.md	.codex/
gemini	GEMINI.md	—
cursor	.cursorrules	.cursor/
windsurf	.windsurfrules	—
cline	.clinerules	—

When you run apply without --agents, an interactive prompt asks which to install for. Agents already present in your target tree (canonical filename or scope dir) are preselected.

Agent scope directories

Some rule repos include agent-specific content that has no equivalent in other agents — e.g. .claude/rules/*.md (Claude Code's path-scoped rules), .claude/commands/*.json, .cursor/rules/*.mdc, .codex/config.toml. Anything inside a recognized scope dir is copied verbatim only when that agent is selected; otherwise the whole subtree is excluded. No renaming or mirroring happens for scoped files — they're already in the format that one agent expects.

Example. Source repo:

.claude/rules/php.md
.claude/commands.json
.cursor/rules/foo.mdc
app/Models/CLAUDE.md

apply --agents claude produces .claude/... + app/Models/CLAUDE.md (skips .cursor/). apply --agents codex produces app/Models/AGENTS.md only (skips both .claude/ and .cursor/).

Source formats

npx apply-agent-rules apply owner/repo                  # GitHub default branch
npx apply-agent-rules apply owner/repo@v1.2.0           # pinned ref
npx apply-agent-rules apply https://github.com/owner/repo
npx apply-agent-rules apply git@github.com:owner/repo.git
npx apply-agent-rules apply ./local-rules-repo

list

Resolves a source (same formats as apply) and prints what it contains without writing anything. Useful for verifying a rules repo before installing.

npx apply-agent-rules list leek/laravel-agent-rules
npx apply-agent-rules list leek/laravel-agent-rules --agents codex,gemini
npx apply-agent-rules list ./local-rules --verbose            # also show excluded

If --agents is passed, each rule file is shown with the destination filenames it would render to.

update

Re-resolves the source from the lockfile and reconciles:

• Unmodified files (local hash matches lockfile) → overwritten with the new source content.
• Locally modified files (drift) → skipped with a warning. Pass --force to overwrite.
• Files removed from source → deleted locally and emptied parent dirs cleaned up. Pass --no-prune to keep them.
• New files in source → added.
• Ref pinning → pass --ref <branch|tag|sha> to move; otherwise re-resolves the source string from the lockfile.

npx apply-agent-rules update                    # re-pull, default prune on
npx apply-agent-rules update --ref main         # change ref
npx apply-agent-rules update --agents claude    # drop other agents, prune their files
npx apply-agent-rules update --no-prune         # keep removed files
npx apply-agent-rules update --force            # overwrite drift, prune modified
npx apply-agent-rules update --dry-run -v       # preview everything

Pass --agents to replace the recorded agent set. Files for dropped agents (rendered files like AGENTS.md, plus their scope dirs like .codex/) are pruned on the same pass. Locally-modified files are kept unless you also pass --force. Pass --no-prune to keep them. Example: switch a project from claude,codex to claude only:

npx apply-agent-rules update --agents claude

Options

apply / add

Flag	Description
-t, --target <dir>	Target project root (default: cwd)
--agents <list>	Comma list of agent ids, or all. Skips the interactive prompt.
-d, --dry-run	Show what would happen
-v, --verbose	Print every file action, including excludes
-f, --force	Overwrite existing files
--include <glob>	Only copy paths matching glob (repeatable)
--exclude <glob>	Skip paths matching glob (repeatable)

update

Flag	Description
-t, --target <dir>	Target project root (default: cwd)
--source <src>	Override source from lockfile
--ref <ref>	Override the ref (branch/tag/sha)
--agents <list>	Replace the agent set; dropped agents' files are pruned
--no-prune	Don't delete files that vanished from source
-f, --force	Overwrite drift and prune locally-modified files
-d, --dry-run, -v, --verbose	as above
--include, --exclude	as above

Built-in excludes

Always skipped: .git/, node_modules/, .DS_Store, **/README.md, **/README, **/LICENSE, **/LICENSE.md, **/LICENSE.txt, .gitignore, .gitattributes, .apply-agent-rules.lock.json. READMEs and license files are treated as repo documentation and skipped at every level. Add more with --exclude '<glob>' (repeatable).

Globs support *, **, ?, [abc], and {a,b,c}. Paths are matched in posix form regardless of OS.

Requirements

• Node 18+
• git on PATH (only for remote sources)

Why not just git clone && cp -r?

You can. This adds:

• Source-format flexibility (GitHub shorthand, refs, ssh, local paths)
• Agent selection — one source-of-truth file, mirrored to N agents' filenames
• A lockfile, so update can detect drift, prune deletes, and refresh without clobbering your edits
• Skip-if-exists semantics so re-applying is safe
• Include/exclude filters, dry-run

License

MIT