Clean Mode

By default, deploy and update remove files found in the destination that don’t exist in the repository — keeping deployed configs in sync with dotfiles/, rather than merely additive.

# Deploy with cleaning (default)
dotr deploy

# Deploy without cleaning extra files
dotr deploy --clean=false

# Update with cleaning (default)
dotr update

# Update without cleaning
dotr update --clean=false

What’s protected from cleaning

• Backup files (.dotrbak extension, see below) are never removed.
• Files matching an ignore pattern for that package are left alone.
• Anything that is part of the current deployment, obviously.

Per-package configuration

[packages.nvim]
src = "dotfiles/nvim"
dest = "~/.config/nvim/"
clean = false  # disable cleaning for this package specifically

clean defaults to true. The --clean CLI flag, when passed, overrides whatever the package specifies for that one invocation; when omitted, the package’s own setting is used.

Backups

When a file at the destination would be overwritten, DotR writes a per-file backup (<file>.dotrbak) alongside it before copying — a lightweight safety net, distinct from dotr update’s job of syncing intentional edits back into the repository. Backup files are always excluded from cleaning, so they won’t be swept away by the same operation that created them.