Repos

mise can declare git repositories in [bootstrap.repos] and apply them with mise bootstrap repos apply or as part of mise bootstrap:

[bootstrap.repos]
"~/src/dotfiles" = { url = "git@github.com:jdx/dotfiles.git", ref = "main" }
"~/src/mise" = { url = "https://github.com/jdx/mise.git" }

Each key is the target path. The url is required. The optional ref can be a branch, tag, or full commit SHA.

Target paths may be absolute, start with ~/, or be relative. Relative paths are resolved against the project root of the config file that declares them and must name a directory inside it — they cannot be empty or ., and cannot escape the root with .. or absolute segments. Because of that, relative paths are only valid in a project config, not in a global config such as ~/.config/mise/config.toml.

Repos run after [bootstrap.packages] and before [dotfiles], so a bootstrap config can install git, clone a dotfiles repository, and then apply dotfiles from that checkout.

Semantics

• Declarative and path-keyed — entries merge across the config hierarchy by expanded target path. A more local config replaces the full repo entry for that path.
• Safe updates only — mise clones missing repos or empty target directories and updates existing repos only when the worktree is clean and the configured origin URL matches. Exactly three network URL forms are compared transport-agnostically: git@host:path, ssh://git@host/path, and https://host/path identify the same repo. Different hosts, ssh aliases, explicit ports, paths, or non-git ssh users still conflict. Everything else requires an exact match: http:// and git:// origins (an insecure transport is never silently treated as the https config), ssh origins without a user (git resolves those to the login user, not git), URLs carrying a query string, local paths, and file:// URLs.
• No implicit writes — repos are changed only by explicit apply, update, exec, or top-level mise bootstrap commands. Applying never pulls an existing repo without a configured ref; use mise bootstrap repos update when you want that imperative behavior.
• No forced resets — dirty repos, non-empty non-git target paths, and mismatched origins fail instead of overwriting local work.
• Omitted ref — an existing repo with the expected origin is considered current; mise does not fetch or update it.

Commands

mise bootstrap repos status            # shows repo checkout state
mise bootstrap repos status --json     # machine-readable
mise bootstrap repos status --missing  # exit 1 if any repo is not current

mise bootstrap repos apply           # clone or update missing/changed repos
mise bootstrap repos apply --dry-run # print the commands without running them
mise bootstrap repos apply --yes     # skip the confirmation prompt

mise bootstrap repos update             # clone missing and pull existing repos
mise bootstrap repos update ~/src/mise  # update only a matching path
mise bootstrap repos update --dry-run   # print the commands without running them
mise bootstrap repos update --yes       # skip the confirmation prompt

mise bootstrap repos exec -- git status        # run argv in every usable repo
mise bootstrap repos exec ~/src/mise -- git pull
mise bootstrap repos exec --continue-on-error -- command
mise bootstrap repos exec --dry-run -- command

update fetches and fast-forward pulls the current branch of repos without a configured ref. It warns and skips an unpinned repo with a detached HEAD. Dirty repos, conflicting origins, and non-git targets fail before any repo is changed. Passing one or more paths limits the update to exact configured paths or their expanded forms.

exec runs the command directly, without shell interpolation, with each repo as its working directory. Missing and conflicting repos are skipped with a warning. It stops on the first command failure unless --continue-on-error is set; in that mode it visits every usable repo and reports all failures at the end.

States

State	Meaning
current	repo exists, origin matches, and ref matches
missing	target path does not exist or is empty
differs	repo is clean but not at the configured ref
dirty	repo has local changes or untracked files
conflict	target path is not the expected git repo