--- title: Cleanup description: Remove stowed links and manually reverse first-use setup changes. --- Use this page when you want to remove the changes `dot` made to a machine. The safe first step is always `dot clean`; everything after that is optional and more destructive. :::caution Review each command before running it. Some steps remove system config, package repositories, cloned repos, or user services. Do not run the whole page as a script. ::: ## Remove stowed links `dot clean` only removes symlinks managed by GNU Stow. It unstows the private overlay first when it is available, then the public packages. ```bash dot clean ``` This does not remove packages, cloned repositories, pacman config, firewall rules, systemd user units, shell changes, generated agent instruction copies, logs, or backup files. ## Restore backed-up files `dot install`, `dot init`, and `dot stow` move conflicting live files into backup paths instead of deleting them. Check the public/private repo backup directories and any Omarchy init backups before removing the repos. ```bash ls ~/.config/dotfiles/backup ls ~/.config/dotfiles-private/backup ls ~/.config/*.dot-init-backup-* ``` Move back only the files you still want to keep. ## Disable user services Disable user timers/services that were enabled from these dotfiles. ```bash systemctl --user disable --now dot-doctor-startup.timer systemctl --user disable --now daily-volume-zero.timer systemctl --user daemon-reload ``` `daily-volume-zero.timer` only exists on laptop stow packages, so that command may report that the unit is missing. ## Remove synced agent instruction copies `dot init` runs `dot agents-sync`, which mirrors the global OpenCode agent instructions into other harnesses. Remove these only if you want those harnesses unmanaged too. Check for the `dot agents-sync` header before deleting anything you may have edited by hand. ```bash grep -H "dot agents-sync" ~/.cursor/rules/global-agents.mdc ~/.claude/CLAUDE.md rm -f ~/.cursor/rules/global-agents.mdc ~/.claude/CLAUDE.md ``` ## Remove managed firewall rules `dot init` adds managed `ufw` allow rules when `ufw` is installed. Delete only the rules you no longer want. ```bash sudo ufw status numbered sudo ufw delete sudo ufw reload ``` The managed rules are labelled in `ufw status` with their purpose, for example KDE Connect, Home Assistant, OpenCode server, LocalSend, and libvirt. ## Remove public pacman repo config Remove the managed include and snippet, then refresh package databases. Do not replace the signed configuration with `TrustAll` or another relaxed signature policy. ```bash sudoedit /etc/pacman.conf sudo rm -f /etc/pacman.d/timmo.conf sudo pacman-key --delete F94469C08E3B717014E2815FA026A3671E9151DA sudo pacman -Syu ``` Remove this line from `/etc/pacman.conf` if present: ```ini Include = /etc/pacman.d/timmo.conf ``` Existing installed packages remain installed. AUR helpers remain available and can build subsequent versions from AUR. To recover a damaged or removed setup, run `dot setup-public-repo`; it downloads the key again and refuses to trust it unless the full fingerprint matches. ## Remove private pacman repo config If `dot setup-private-repo` or `dot init` registered the private package repo, remove the include line and snippet manually. ```bash sudoedit /etc/pacman.conf sudo rm -f /etc/pacman.d/timmo-private.conf sudo pacman -Sy ``` Remove this line from `/etc/pacman.conf` if present: ```ini Include = /etc/pacman.d/timmo-private.conf ``` If your private config overrides `DOT_PRIVATE_PACMAN_REPO_CONFIG` or `DOT_PRIVATE_PACMAN_MAIN_CONFIG`, use those paths instead. `dot setup-private-repo` also syncs a local `file://` mirror from the private package repo config. If you want to remove that mirror and source clone too, check `path=` and `mirror_path=` in `~/.config/dotfiles-private/.dot-private-package-repo` and remove only those directories. ## Remove pacman hooks Public/private pacman hooks are installed into `/etc/pacman.d/hooks` from stowed hook sources. Remove only hooks that came from these dotfiles. ```bash ls ~/.config/pacman-hooks ls /etc/pacman.d/hooks sudo rm /etc/pacman.d/hooks/.hook ``` ## Restore the login shell `dot init` sets the login shell to zsh when needed. Change it back if you no longer want zsh as the login shell. ```bash chsh -s /bin/bash "$USER" ``` If init added `/usr/bin/zsh` to `/etc/shells`, leave it unless you know nothing else on the machine needs it. ## Remove Git config include `dot init` adds the managed Git include to your global Git config. Remove it if you no longer want Git to load the stowed dotfiles settings. ```bash git config --global --fixed-value --unset-all include.path "~/.config/git/config.dotfiles" ``` ## Revert generated locales `dot init` ensures `en_GB.UTF-8` is enabled in `/etc/locale.gen` and runs `locale-gen`. Leave the locale in place unless you specifically want to remove it. ```bash sudoedit /etc/locale.gen sudo locale-gen ``` ## Remove cloned repos and state After the stowed links and system config are removed, delete cloned repos and generated state only if you no longer need them. ```bash rm -rf ~/.config/dotfiles-private rm -rf ~/.local/state/dot ~/.cache/dot ``` Private package repos and other private Git clones are configured by the private overlay. Review `~/.config/dotfiles-private/.dot-private-package-repo` and `~/.config/dotfiles-private/dot-git.yml`, then remove only clones and mirrors you no longer need. If you removed stowed config directories that Omarchy should own again, refresh the stock Omarchy defaults afterwards. Quattro's UWSM defaults are package-owned under `/usr/share`, so there is no `uwsm/env` user config to refresh. ```bash omarchy refresh shell omarchy refresh hyprland omarchy refresh config ghostty/config ``` Run `omarchy refresh --help` on the target machine for the exact refresh commands supported by that Omarchy version. Do not remove `~/.config/dotfiles` until you no longer need the `dot` binary, docs, or backup directory. ## Remove installed packages `dot init` installs the public/private package lists but does not track ownership of packages afterwards. Removing packages is intentionally manual. This command only covers the default public package list; if you override `DOT_PUBLIC_PACKAGES_FILE`, use that file instead. ```bash comm -12 <(sort ~/.config/dotfiles/.dot-public-packages) <(pacman -Qq | sort) ``` Review that output, then remove only packages you no longer use. ```bash sudo pacman -Rns ``` For private packages, review the private package list before removing anything. `dot install` and `dot init` may also install setup prerequisites such as `stow`, `gum`, or `mise-bin` when they are missing. Remove those manually only if nothing else uses them. ## Remove mise-managed tools `dot init` runs `mise install`, which can install language and CLI tool versions from the stowed mise config. Remove only versions you no longer use. ```bash mise ls --installed mise uninstall ``` ## Remove GitHub CLI extensions `dot init` installs the GitHub CLI extensions listed in `.dot-gh-extensions` when `gh` is available. Remove only extensions you no longer want. ```bash gh extension list gh extension remove ``` ## Final check Run doctor after cleanup to see what managed state remains. It will report missing dotfiles pieces if the repo is partly removed, which is expected during a full uninstall. ```bash dot doctor ```