Reconcile behavior

Each package source has a different convergence model. The important question is whether removed declarations also remove installed tools.

Manager behavior

Manager	Installs / updates	Removes when deleted from list?	Notes
Homebrew	brew bundle --global --no-upgrade	Yes, via brew bundle cleanup --global --force	assembled Brewfile is authoritative; installs missing only (upgrades owned by ,update)
mise	mise install --yes, then mise reshim	No cleanup of old runtimes by this hook	respects project .tool-versions; Node reads .nvmrc
Cargo	installs missing crates	Yes	hook uninstalls crates no longer listed
Go	installs missing module binaries	Yes, but only binaries this tooling installed	state ledger at ~/.cache/chezmoi/golang-pkgs-state protects hand-installed binaries
Ruby gems	installs listed gems	No	hook does not uninstall gems removed from the list
yarn	installs missing globals, uninstalls absent globals, upgrades latest	Yes	avoids Yarn v1 staying on old 0.x ranges
uv Python	installs listed managed Python versions	Yes	hook uninstalls managed Python versions absent from home/readonly_dot_python-version
uv tools	installs listed global tools	managed by uv tool hook	tool source is home/readonly_dot_default-uv-tools.tmpl
gh extensions	installs managed extensions	Yes	hook prunes extensions no longer listed
Custom packages	downloads GitHub release assets, DMGs, or source builds	Partial	stale launchers/repos are cleaned when safe; dirty source repos are preserved

Notable package decisions

Decision	Reason
Homebrew link: false for colliding sem binaries	GNU parallel and Ataraxy semantic-git both expose sem; wrappers expose the intended ,parallel and ,sem commands
Pi globals live in yarn	@earendil-works/pi-coding-agent, @earendil-works/pi-tui, pi-mcp-adapter, and pi-subagents are kept together in the managed yarn list
Custom installer includes ytsurf	installed outside standard package managers in this setup
git_maven_jar rows are declarative	add/update rows clone/build/install; removed clean repos are deleted; dirty stale repos are preserved

Where to make changes

Goal	Start here
Add or remove a Homebrew package	Add a Homebrew package
Pin a runtime	Pin a tool version
Add a language-specific CLI	Cargo / Go / Ruby / yarn / uv recipe pages
Add a GitHub release binary or DMG	Custom packages registry