The file-safety contract

When you install a pack from this catalogue, the install verb writes files into your repo — AGENTS.md, docs/CHARTER.md, skill directories, hooks. If you’ve already edited any of those files (or the upgrade you’re running has new content for them), what happens?

The short answer: your edits are never silently overwritten. This page explains the long answer — what mechanism makes the guarantee hold, how it differs by install route, and where the contract is authoritative.

The three tiers

The catalogue models every path in your repo as one of three tiers:

• Tier-1 — files the catalogue writes and considers its own. The pack’s seeds and projections. On install, these can be written freely; on upgrade, they’re replaced if the on-disk content matches what the catalogue last wrote (i.e. you haven’t edited it).
• Tier-2 — files the catalogue wrote and you subsequently edited. The CLI tracks this by hashing every projected file at install time into .agentbundle-state.toml; on upgrade, a hash mismatch means Tier-2.
• Tier-3 — files outside the pack’s projected paths. Your source code, your own docs/<thing>.md that no pack ships, your .gitignore, your CI config. The catalogue never reads, writes, or even acknowledges these.

The guarantee in one sentence: the install and upgrade verbs touch Tier-1 only. Tier-2 collisions land as companions; Tier-3 files are invisible.

What the catalogue actually does on collision

First-install collision (CLI route)

If agentbundle install would write AGENTS.md and you already have one, it drops AGENTS.upstream.md next to yours and leaves your AGENTS.md alone. The adapt-to-project skill picks up these companions and proposes a merge per file — accept, edit, skip, or decline.

Upgrade collision (after CLI install or agentbundle init-state)

The CLI records a SHA-256 of every projected file in .agentbundle-state.toml at install time. On the next agentbundle upgrade --pack <name> <catalogue>, any file whose content diverged since install (Tier-2) gets a *.upstream.<ext> companion dropped next to it; your edited file is left alone and the CLI continues without prompting. The upgrade then reports on stderr how many files were kept and the companion path of each, so you can find them. The merge UI lives in the adapt-to-project skill, which you re-invoke after the upgrade to walk the new companions one at a time. The CLI never clobbers or prompts; the keep/merge/overwrite choice lives in adapt-to-project.

Tier-3 (everything else)

Untouched on install and on upgrade — including files in directories the catalogue does write to but at sibling paths the catalogue doesn’t claim (your docs/your-decisions.md next to the pack’s docs/architecture/overview.md, for instance).

Scope of the guarantee — by install route

The contract binds the agentbundle CLI’s install path and the adapt-to-project skill. APM (apm install) and Claude Code plugins (/plugin install) are governed by those tools’ native file-handling semantics; the catalogue cannot intercept them.

The three routes differ:

Route	Install-time safety	Upgrade-time safety
agentbundle install (CLI)	Companion drop on Tier-2 collision.	Companion drop on Tier-2 divergence (.agentbundle-state.toml is the baseline).
apm install	APM’s own conflict rules apply (it compiles straight to the working tree).	Same — unless you ran agentbundle init-state once after the install, which hashes the just-installed files. From that point forward the catalogue contract applies.
/plugin install (Claude Code)	Install-time collisions don’t arise (plugins install into a Claude-managed cache, not your working tree).	Re-emerge only if you copy the cached files into your tree by hand — in which case run agentbundle init-state first if you want catalogue-level safety on subsequent upgrades.

If you installed via APM or a Claude plugin and want the catalogue’s upgrade-safety guarantee, the one-time gesture is:

agentbundle init-state

This walks the projected paths the catalogue knows about and hashes each into .agentbundle-state.toml. After that, agentbundle upgrade behaves identically across all three install routes.

Seeds, by install route

The Tier model above applies to seeds (AGENTS.md, docs/CHARTER.md, governance docs) the same as to projected primitives — but which route lands them in your working tree differs, and this is the same CLI-vs-cache split as above:

• CLI route (agentbundle install) writes the seeds directly into your repo (repo root and docs/) with the first-install companion behaviour described above, and records them in .agentbundle-state.toml.
• APM and Claude-plugin routes ship the seeds inside the installed artifact (the APM package / the Claude-managed plugin cache), but do not place repo-root governance docs in your working tree — the plugin cache and APM HookIntegrator project primitives, not seeds, and the install-marker SessionStart hook writes only the marker. To land the seeds, run agentbundle install or agentbundle scaffold --pack <name> --output . (the agentbundle CLI those routes already need on PATH).

A session-time auto-copy of seeds out of the plugin cache would cross the “the catalogue cannot intercept APM/plugins” line above; it is deliberately not done.

Why this exists

The simplest alternative would have been: overwrite Tier-1 files on install, ask the adopter to put AGENTS.md and docs/CHARTER.md into .gitignore if they want to edit, and let git diff handle the rest. We rejected that because the files the catalogue ships are deliberately the ones adopters need to edit — AGENTS.md is the project’s agent context; docs/CHARTER.md is the project’s own mission statement. Asking an adopter to gitignore those is asking them not to use the catalogue’s most load-bearing seeds.

Tier-2 + companions are the design that lets the catalogue ship opinionated seeds and respect adopter edits — both, not either-or. The cost is a slightly more involved merge step (the adapt-to-project skill), which is worth it because the alternative (silent overwrite) destroys trust on the first upgrade.

Related

• How to adapt a freshly-installed pack — the skill that walks *.upstream.<ext> companions.
• How to upgrade an installed pack — the verb that produces upgrade-time companions.
• docs/CONVENTIONS.md § Pack source-of-truth split — the internal mirror of the Tier model, for contributors.