[geekgonecrazy]

What

atomic agent enable used to fail with RepositoryNotFound outside an Atomic repository. Nothing about enabling needs a repo, though: every installed hook command is guarded by test -d .atomic || test -f .atomic-sandbox && ..., so hooks stay dormant until they fire inside an Atomic repository. This PR removes the requirement.

What enabling actually does (and why the fallback targets home)

Every registry agent resolves to an integration package, and the packages install entirely into the home directory per their manifests — ~/.claude/settings.json, ~/.config/opencode/opencode.json, ~/.claude/skills/..., ~/.config/opencode/plugins/atomic-hooks.ts, agent prompt slots — never the repo. The repo root only feeds:

• agent auto-detection (registry.detect, when no --agent)
• .atomic/sessions/ creation
• [[repo-file]] entries (e.g. AGENTS.md), and only with --agents-md

The repo-relative AgentHook::install path in run() is a degraded fallback for when the package cannot be fetched. This PR makes that fallback degrade to the home directory (where the packages install anyway) instead of failing:

• run — find_repository_root()? falls back to the home directory as the install base when no repo is found, printing warnings that turns are only recorded in projects with a .atomic/ directory.
• .atomic/sessions/ — only created when a repo was found, so the fallback path never touches ~/.atomic/ (global config).
• --agents-md — the second find_repository_root()? (in install_integration, for [[repo-file]] entries) now skips those entries with a warning instead of failing the whole install. InstallOptions.repo_root was already Option<PathBuf>, so None slots in cleanly.
• Docs corrected in enable.rs and agent/mod.rs to state all of the above.

Inside a repository, behavior is unchanged: same base directory, same sessions directory, no fallback warnings.

Verification

All e2e runs used a HOME override so the real ~/.claude/settings.json was untouched.

• cargo check -p atomic-cli — clean
• All 103 commands::agent tests pass
• E2E outside any repo: hooks install into $HOME/.claude/settings.json, nothing in cwd, no .atomic/sessions anywhere
• E2E inside a fresh atomic init repo: no fallback warnings, .atomic/sessions/ created, 8 hooks in the repo's .claude/settings.json (via the built-in fallback — see note), nothing in $HOME

Note

While testing I hit a pre-existing failure unrelated to this change: the claude-code integration package install exits non-zero ("partial install") because the cloned atomic-skills release view is missing atomic-integration.toml and AGENTS.md at its root (they exist in the local checkout at ~/code/work/atomic-skills, which is pushed, so the storage release view looks stale). It reproduces identically inside and outside a repo, so it predates this PR — happy to dig into it separately.

[geekgonecrazy]

Follow-up: removed the redundant --global path entirely.

Why: the integration packages (the normal enable path for every registry agent) install entirely into the home directory and never the repo. The pre-package --global path was a parallel, worse model — bare hooks only, no skills, no prompts, no receipt. With plain enable now falling back to the home directory outside a repository, one install model remains and --global only added confusion.

Removed:

• --global flag from agent enable and agent disable (clap now rejects it on both)
• both run_global() implementations
• orphaned install_global/uninstall_global on claude/gemini/codex hooks and claude/gemini global_settings_path in atomic-agent (codex keeps global_hooks_path/is_installed_global — its trait is_installed and the receipt-repair path still use them)

disable got simpler and more complete:

• same outside-repo fallback as enable (home directory, with a warning)
• one disable now cleans both scopes — the uninstall base and the home config — so legacy global installs that predate receipts are also removed
• agents_with_installs unions repo-base, home, and receipt-discovered agents

Net: 6 files, +72/−555. Marked refactor! with a BREAKING CHANGE note for the flag removal.

Verified:

• --global rejected by clap on both commands (exit 2)
• outside a repo: enable puts 8 hooks in $HOME/.claude/settings.json; plain disable removes all of them (reports the base path per agent)
• inside a repo with hooks in both repo and home config: one disable reports both removals and leaves zero hooks in either
• 101 CLI agent tests + 28 atomic-agent tests pass; clippy and fmt clean (all e2e against a HOME override — real ~/.claude untouched)