Documentation #

Only what cannot be discovered by running the tool or reading the code. Flags and defaults are in atgc <command> --help. What a command prints is in its output. Why a dependency is vendored is in Cargo.toml. What changed and when is in git log. What is enforced is in prek.toml. None of that is repeated here, because a second copy is a second thing to be wrong.

What is left is six pages:

1. The model. Tangled's shape, which is somebody else's system and cannot be read out of this repo. Start here; nothing else makes sense first.
2. Who atgc acts as. Which account a command publishes under, how a worktree gets one of its own, and how to give several agents several identities.
3. Output contracts. The five rules that hold for every command.
4. Module layout. Where code goes, and the rules that are not visible from the folder names.
5. Testing. What earns a test, and when to reach for a mock.
6. Environment. Every ATGC_* variable, including the ones no --help page names.

These are CommonMark under docs/, also compiled into rustdoc by src/docs.rs, so a reference from prose into code is checked at build time. cargo docs builds it. Code fences need a language tag and must not be rust; prek explains why when it stops you.