Chezmoi Management

chezmoi Management (mizchi personal)

Personal dotfiles operations notes. The official chezmoi docs are already sufficient, so this document focuses solely on how things concretely work in my own environment.

Baseline environment

Responsibility split with nix home-manager

This repo runs alongside home-manager — neither is a superset of the other:

• home-manager owns: CLI packages (home.packages), programs.* wrappers (git / direnv / zsh / etc), and tool installs that flow through Nix derivations (e.g. pkfire, pkl, actionlint, awscli2, pkgs.go). Edit dot_config/home-manager/common.nix then darwin-rebuild switch --flake .#macos (or home-manager switch).
• chezmoi owns: dotfile content that programs.* can't shape — ~/.claude/, ~/.codex/, ~/.apm/, ad-hoc ~/.config/<editor-or-shell>/, ~/.zshrc, kept-templated paths.
• APM owns: public Claude Code skills under ~/.claude/skills/<name>/. .chezmoiignore lists each APM-managed skill so chezmoi never re-deploys over apm install -g.

Rule: if a programs.* wrapper exists in home-manager for a tool, configure it there — do not also stage the dotfile via chezmoi. Mixing creates two source-of-truth conflicts that surface as "I edited the file but my change keeps reverting".

Layout cheat sheet

~/.local/share/chezmoi/
├── dot_apm/          → ~/.apm/      (APM config)
├── dot_claude/       → ~/.claude/   (Claude Code)
│   ├── CLAUDE.md.tmpl
│   ├── settings.json.tmpl
│   ├── rules/
│   └── skills/       → ~/.claude/skills/   (self-authored skills)
├── dot_codex/        → ~/.codex/
├── dot_config/       → ~/.config/   (helix, mise, sheldon, starship, zellij, zsh, home-manager)
│   └── home-manager/ → ~/.config/home-manager/  (flake.nix / common.nix / darwin.nix — Nix-evaluated; chezmoi only stages the files, Nix does the actual install)
├── dot_zshrc         → ~/.zshrc
├── run_once_before_install-brew.sh   (bootstrap: clone Homebrew prefix to ~/brew before nix-darwin first activation)
└── run_after_apm-install.sh          (every apply: apm install --global --target claude)

Meaning of filename prefixes

Daily flow

(1) Check what differs

chezmoi diff                   # diff between source and dest
chezmoi status                 # rough status (MM/M /?? etc.)

Direction sense for chezmoi diff: the output is in - dest / + target order (following git diff's old=current / new=after-apply convention).

• - lines = content in dest (the current real file) — will be removed by apply
• + lines = content in target (the expected state after source.tmpl expansion) — will be added by apply
• chezmoi apply moves in the direction of aligning dest to target (source → dest)

When in doubt, the fastest way to confirm is to look at both cat <source> and cat <dest>.

The columns for chezmoi status are [source][dest]:

• M = modified, A = added, D = deleted, ? = untracked (not in source)
• MM → changes on both sides (need to absorb the manually-edited dest into source)
• M → source unchanged but dest was modified (stray change)
• DA → marked as deleted in source but exists in dest (junk like node_modules/)

(2) Edited dest (the real file) → absorb into source

chezmoi add ~/.zshrc                    # add a new file
chezmoi re-add                          # bulk-reflect changes from managed dest into source
chezmoi re-add ~/.claude/CLAUDE.md      # individual

(3) Edited source (repo side) → apply to dest

chezmoi diff                            # look first
chezmoi apply                           # all
chezmoi apply ~/.claude/CLAUDE.md       # individual
chezmoi apply --verbose                 # show what it's doing

(4) Open source in an editor

chezmoi edit ~/.zshrc                   # open the source side (whether to apply after closing the editor is controlled by the -a flag)
chezmoi edit -a ~/.zshrc                # also run apply after editing
chezmoi cd                              # cd to source dir

New machine initialization

Install order is nix → chezmoi → apm. brew prefix is bootstrapped by chezmoi's run_once_before_install-brew.sh so nix-darwin's homebrew module can reference ~/brew on first activation.

# 1. Install Nix (Determinate Systems installer recommended).
curl -fsSL https://install.determinate.systems/nix | sh -s -- install

# 2. Bootstrap chezmoi (clones repo + applies; the brew script runs once here).
chezmoi init https://github.com/mizchi/chezmoi-dotfiles.git --apply

# 3. Switch home-manager / nix-darwin (installs pkfire, pkl, awscli2, …).
nix run nix-darwin -- switch --flake ~/.config/home-manager#macos
# (or for standalone HM without system-layer changes:
#  nix run home-manager/master -- switch --flake ~/.config/home-manager#macos)

# 4. Arm the pre-push gate on this repo's source.
cd $(chezmoi source-path)
pkf hooks install   # writes .git/hooks/pre-push (secretlint over outgoing diff)

# 5. apm install -g already fired via run_after_apm-install.sh during step 2.
#    To pick up upstream updates later: apm install -g --update

Skill-addition flow (my personal routine)

1. Develop and verify in ~/.claude/skills/<name>/ (for nix-setup, get nix build passing)
2. chezmoi add ~/.claude/skills/<name> to reflect into source
   • Scripts with +x get the executable_ prefix automatically
3. cd ~/.local/share/chezmoi && git status to confirm added files
4. git add dot_claude/skills/<name>/ + commit + git push origin main

If you edited an existing skill

Both chezmoi add and chezmoi re-add overwrite. In practice, re-add tends to produce fewer extraneous diffs:

chezmoi re-add ~/.claude/skills/nix-setup/SKILL.md

APM vs chezmoi boundary

~/.claude/skills/ is a mix of two systems:

Currently installed via APM (excerpt from dot_apm/apm.yml):

• moonbitlang/moonbit-agent-guide/* (moonbit-agent-guide, moonbit-refactoring, moonbit-c-binding)
• mizchi/moonbit-practice/skills/moonbit-practice
• mizchi/flaker/skills/flaker-setup
• ast-grep/agent-skill/ast-grep
• mizchi/tui.mbt/skills/tuimbt-practice

Decision criteria:

• Public / likely to be used from other repos → place in the upstream repo and register with APM
• Operational notes used only in my own environment / experimental skills → chezmoi-managed

If a directory of the same name exists in both locations, APM may overwrite it at install time, so watch out for name collisions.

Check for APM name collisions before adding a new skill to chezmoi:

# Check whether the same name exists on the APM side
grep "<skill-name>" ~/.local/share/chezmoi/dot_apm/apm.yml
# or
chezmoi cd && grep -r "<skill-name>" dot_apm/

Editing tmpl files

CLAUDE.md.tmpl and settings.json.tmpl are Go templates:

chezmoi edit ~/.claude/CLAUDE.md     # opens the source-side .tmpl, not the real file
chezmoi execute-template < foo.tmpl  # manually check the expansion result
chezmoi data                         # list data available for expansion (hostname, OS, etc.)

Examples of template variables: {{ .chezmoi.os }}, {{ .chezmoi.hostname }}

Caution: Running chezmoi re-add against a .tmpl-managed file (CLAUDE.md.tmpl, settings.json.tmpl, etc.) will overwrite the .tmpl syntax in source with the expanded dest content. To update a .tmpl file, use chezmoi edit (which automatically opens the .tmpl side) or edit ~/.local/share/chezmoi/dot_claude/CLAUDE.md.tmpl directly.

Pre-check before re-add: always check whether the target file is .tmpl-managed with chezmoi source-path:

chezmoi source-path ~/.claude/CLAUDE.md
# → /Users/mz/.local/share/chezmoi/dot_claude/CLAUDE.md.tmpl
# If it ends in .tmpl, don't re-add — edit manually. If not .tmpl, re-add is OK

When you want to change the default value of a tmpl variable

Rather than rewriting the tmpl itself to a hard-coded value, put the variable in the [data] section of ~/.config/chezmoi/chezmoi.toml:

[data]
  claude_default_mode = "auto"
  github_username = "mizchi"

It's more flexible to preserve tmpl structures like {{ .claude_default_mode | default "acceptEdits" }} as-is and switch only the values per-host via [data] (leaves room to vary settings across machines).

pre-push (pkfire + secretlint)

secretlint runs on git push via pkfire (Taskfile.pkl → pkf hooks install → .git/hooks/pre-push), scoped to the diff range about to be pushed. Diffs containing API keys or tokens are rejected.

Re-arm the hook on a fresh checkout with pkf hooks install. Emergency bypass: git push --no-verify.

Common false positives:

• Example sha256 / hex strings (can trip when length resembles aws keys / github tokens)
• Sample values written in .envrc comments

Remediation:

# If it really is a false positive, exclude the rule in .secretlintrc.json
# If the detection is correct, fix the line and git add ... && git commit

Exclusion syntax in .secretlintrc.json (excerpt):

{
  "rules": [
    {
      "id": "@secretlint/secretlint-rule-preset-recommend",
      "options": {
        "allows": [
          "/sha256-[a-f0-9]{64}/",
          "fake-token-for-example",
          "skill-examples/*"
        ]
      }
    }
  ]
}

allows takes either a regex (surrounded by /.../) or a literal string match. Per-file exclusion is possible via disabledRules + includes/excludes.

Don't use --no-verify (defeats the purpose).

Troubleshooting

chezmoi status shows a flood of DA (node_modules/ etc.)

Append to .chezmoiignore:

node_modules
**/.DS_Store

source and dest conflict

chezmoi merge ~/.zshrc          # 3-way merge (vimdiff-style)
chezmoi forget ~/.something     # remove from source (keep dest)
chezmoi destroy ~/.something    # remove both (destructive)

The chezmoi merge backend is configured in the [merge] section of ~/.config/chezmoi/chezmoi.toml:

[merge]
  command = "nvim"
  args = ["-d", "{{ .Destination }}", "{{ .Source }}", "{{ .Target }}"]

If unset, chezmoi consults git config merge.tool. If both are unset, it falls back to vimdiff.

Apply broke things → roll back to a previous revision

chezmoi itself has no undo. Roll back via git on the source side:

chezmoi cd
git log --oneline -5
git reset --hard <rev>
cd -
chezmoi apply

Which files are managed

chezmoi managed                 # list of managed files
chezmoi unmanaged ~/            # unmanaged files
chezmoi managed ~/.claude       # filter by path

apply is slow

apm install inside run_after_apm-install.sh runs every time. If no skill updates are needed, skip it via an env var at apply time:

SKIP_APM=1 chezmoi apply    # only if the script supports it (otherwise ignored)

If unsupported, ignore.

Reference command cheat sheet

chezmoi diff                    # diff
chezmoi status                  # status
chezmoi apply [-v]              # apply
chezmoi add <path>              # take in a new file
chezmoi re-add [<path>]         # re-take an existing file
chezmoi edit [-a] <path>        # edit source (-a applies immediately after)
chezmoi merge <path>            # 3-way merge for conflicts
chezmoi forget <path>           # drop from source
chezmoi managed [<path>]        # list managed files
chezmoi unmanaged <path>        # unmanaged files
chezmoi cd                      # cd to source-path
chezmoi source-path             # show source directory
chezmoi execute-template <     # test template expansion
chezmoi data                    # list variables usable in templates
chezmoi doctor                  # setup diagnosis