[jdx]

https://entire.io/gh/jdx/mise/trails/415

Requested by Jeff

Many dotfiles repositories are laid out like GNU Stow packages: one directory per application or machine role, each deployed into ~. Until now, every tree needed its own [dotfiles] entry, and a machine could not choose which trees to apply. Dotfile groups add both (from discussion #13934).

[dotfile_groups.zsh]
root = "zsh"                     # ~/.dotfiles/zsh, walked into ~

[dotfile_groups.home]
root = "home"
dot_prefix = true                # dot-config/ deploys as .config/
exclude = ["README.md"]

[dotfile_groups.home.entries]    # ordinary whole-file entries, cut out of the walk
"~/.config/kitty" = { mode = "symlink" }                            # link this directory whole
"~/.gitconfig" = { source = "git/config.tmpl", mode = "template" }  # relative to the root
"~/.kitty-old.conf" = { mode = "absent" }

[bootstrap]
dotfile_groups = ["home", "zsh"]   # unset: every group applies

What groups do

• Group trees. [dotfile_groups.<name>] requires a root. A relative root resolves against dotfiles.root, not the declaring file's directory. Other keys: target (default ~), mode (symlink-each by default, or copy or symlink), exclude, dot_prefix, manifest, relative. mise walks the root and deploys each file at the same path under the target, so you don't list files. A more local config's table replaces the whole group.
• Group entries. [dotfile_groups.<name>.entries] uses the same syntax as [dotfiles], keyed by target, and each entry is cut out of the walk. This is how a directory is linked whole, a file rendered as a template, copied with permissions, removed with absent, and so on.
  • An entry without source finds it under the root at its path inside the group target; a relative source starts at the root, and a source inside the root is not also deployed by the walk.
  • An entry without mode deploys like the group: a file as one link, or as one copy in a copy group.
  • Walking entries inherit the group's dot_prefix, manifest, and its exclude patterns without /.
  • Entries must lie inside the group target. An entry beneath a directory linked whole would change a file in the root itself, so it fails as a conflict before anything is written.
• [dotfiles] entries take no group. They always apply, and entries belong to a group only by being declared under it.
• Selection. [bootstrap] dotfile_groups chooses the groups a machine applies; the most local list wins. If the list names a group that nothing declares, mise warns.
• Conflicts. If two selected groups write the same file, or one links a directory another writes into, apply and status fail before anything is written. The error names both groups. Two groups with the same tree conflict too.
• Orphans and removal. Each apply records what a group deployed in $MISE_STATE_DIR/dotfiles/groups/, including after a partial failure. mise dot status lists as orphaned every recorded file that no active entry deploys now: from a deselected or deleted group, or one a selected group stopped deploying (a new exclude, a removed entry, the copy of a deleted source). mise dot apply --prune removes them after asking, unless --yes. mise dot unapply --group <name> removes one group's files even after the group is gone from config. Both go by what mise last wrote, not the current source. They remove links still pointing at their source and copies still holding the recorded contents; --force also removes changed copies. They never remove a path another active entry deploys, a path reached through a linked directory, or a path inside dotfiles.root, even with --force, and on Unix the delete walks directories without following links.
• mise dot add and mise dot edit route into groups. A file under a group's target is captured into, or edited in, that group's root, with a dot- name in dot_prefix groups, and no entry is written. mise picks the group with the deepest target, then the one whose root already holds the file; for a new file it asks for --group, which both commands accept. edit --apply applies only that file, and only if the group's walk deploys it. [dotfiles] edit keys like ~/.zshrc/activate take precedence. Groups with manifest = "git" refuse captures.

Notes

• mise oci build reads only [dotfiles] entries scoped to the project, so it does not include group trees.
• Not in this PR: bootstrap --from --config-root, and the Windows unapply-planner fix for symlink-each file links.

Validation

• New e2e e2e/cli/test_dotfiles_groups: applying all groups, entries (whole-directory links, templates with root-relative sources, absent, copies), selection, orphan status, unapply --group, apply --prune, routing add into a dot_prefix group, --group ambiguity, conflicts, required roots, and group rejected on [dotfiles].
• New e2e e2e/cli/test_dotfiles_groups_ownership: editing grouped files, removal by saved ownership, files a group stops deploying, a declaration moved between groups, two groups with one tree, missing roots, manifest = "git", removal never following a linked directory (fails against the earlier code), edit keys and edit --apply scoping, and tracked files.
• Unit tests for group names, dot- source naming, exclusion escaping, and rejecting group in pulled-in config.
• cargo clippy --workspace --all-features --all-targets -- -D warnings, mise run lint-fix.

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---

Note

Medium Risk
Changes dotfile apply/unapply behavior and can delete user files via prune and group unapply, though guarded by ownership checks and extensive e2e coverage.

Overview
Adds dotfile groups — named directory trees under [dotfile_groups.<name>] (Stow-style layouts) that machines can turn on via [bootstrap] dotfile_groups, with per-group entries overriding parts of the walk.

Config & core: New dotfile_groups module expands groups into tagged FileRequests, records deployments under $MISE_STATE_DIR/dotfiles/groups/, detects orphaned files when groups are deselected or stop deploying, and removes them with conservative ownership checks (symlink/digest, no following links into sources).

CLI: mise dot apply --prune, unapply --group, add --group, and edit --group; status/JSON report orphans. add/edit route captures into group trees without new [dotfiles] entries.

Docs, JSON schema, usage/man pages, and two e2e suites cover selection, conflicts, pruning, and removal safety.

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Summary by CodeRabbit

• New Features
  • Organize dotfiles into named groups with configurable deployment settings, and choose which groups to apply on each machine. All groups apply by default when no selection is configured.
  • Use --group with dotfile add and edit to target a group, or with unapply to remove only that group’s files.
  • Use apply --prune to remove files left behind by deselected or removed groups. Status reports these files as orphaned; changed files are preserved unless forced.
• Documentation
  • Updated command help, examples, and configuration guidance for dotfile groups and their lifecycle.

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📒 Files selected for processing (4)

• e2e/cli/test_dotfiles_groups
• e2e/cli/test_dotfiles_groups_ownership
• src/system/dotfile_groups.rs
• src/system/files.rs

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📝 Walkthrough

Walkthrough

This change adds named dotfile groups, group selection, group-aware capture and editing, deployment records, orphan reporting, pruning, and group-scoped removal.

Changes

Dotfile groups

Layer / File(s)	Summary
Group configuration and request composition schema/mise.json, src/config/config_file/*, src/system/dotfile_groups.rs, src/system/files.rs, src/system/mod.rs	Adds group definitions, selection rules, tree expansion, validation, conflict handling, and group-aware file requests.
Capture and edit files through groups src/cli/dotfiles/add.rs, src/cli/dotfiles/edit.rs, docs/cli/*/dotfiles/{add,edit}.md, e2e/cli/test_dotfiles_groups*	Adds --group routing for add and edit. New targets can be captured into matching group sources without creating a [dotfiles] entry.
Apply, inspect, and remove group deployments src/cli/dotfiles/{apply,status,unapply}.rs, src/system/dotfile_groups.rs, e2e/cli/test_dotfiles_groups*	Records group deployments, reports inactive paths as orphaned, and adds apply --prune and unapply --group with ownership checks.
Documentation and generated help docs/dotfiles.md, docs/bootstrap.md, docs/cli/**, man/man1/mise.1, mise.usage.kdl	Documents group configuration, selection, capture, editing, orphan reporting, pruning, and group-scoped removal.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~60 minutes

Change: Feature

Merge Risk: 🔵 Low · up to c14d2

A narrow cleanup case can leave a formerly deployed file outside group tracking. This is mergeable with a follow-up to preserve that record.

Security Architecture Review

Security architecture risk: 🟡 Moderate · up to c14d2

Ownership and path checks limit destructive cleanup, but deployment records are not recovered together with files. Disabling history also removes command serialization while those records remain mutable. These gaps can leave rollback and later cleanup inconsistent.

Retained concerns

• Medium · reliability · inferred: Group-record changes are not journaled with filesystem changes. If group cleanup removes a file and updates its record before the process is interrupted, recovery can restore the file without restoring its group ownership entry. A deleted or deselected group can then leave restored deployments undiscoverable by later cleanup. Recovery after apply can likewise leave post-apply ownership metadata beside restored pre-apply contents. Atomic record writes and ordinary-error handling do not restore this pairing; non-forced ownership checks generally contain the mismatch by refusing removal.
• Low · reliability · inferred: With history.enabled=false, apply and unapply enter inactive operation scopes and do not acquire the operation lock. Group records are still updated through load-modify-save sequences without their own serialization. Concurrent commands can replace one another's updates and lose deployment ownership entries, weakening later cleanup. The operation lock protects the normal history-enabled path, and atomic replacement protects file integrity, but neither covers this disabled-history path.

Security review details

Security Blast Radius

• inferred — Effective exposure is the filesystem accessible to the invoking process, not necessarily only its home directory: configuration can choose absolute sources and targets. Group entry containment limits entries to their chosen group target, but is not a process sandbox. This configured filesystem authority already exists in the ordinary deployment pipeline; no new privilege elevation was established.

Trust Boundaries and Controls

• observed — Records reside under MISE_STATE_DIR, defaulting to the user's XDG state location. Loading validates format version and group identity, but does not authenticate record provenance. Cleanup therefore relies on the state directory being controlled by trusted writers; actual deployment ownership and access permissions were not established.
• observed — Group cleanup excludes paths claimed by other active entries. Force broadens removal to changed digest-recorded non-directories, but does not bypass the path-safety checks. This is explicit additional deletion authority, not evidence of a newly verified attack path.

Resilience and Maintainability Implications

• observed — History-enabled operation scopes hold an operation lock and recover interrupted journaled changes. Recovery refuses unmatched completion state or subsequent edits rather than overwriting them. These controls contain filesystem recovery, but do not reconcile the separate group-record lifecycle.

Hardening Proposals

• proposed — Coordinate group-record changes with recoverable filesystem transitions, and serialize ownership updates independently of optional history recording. This would preserve cleanup provenance through interruption and concurrent commands without weakening existing removal checks.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 69.89% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 93 functions across 14 files. (2 skipped:…	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: adding dotfile groups.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

Full details: Docstring Coverage

Explanation

Docstring coverage is 69.89% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 93 functions across 14 files. (2 skipped: 2 unsupported.)

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[greptile-apps]

Confidence Score: 5/5

[Medium risk] Adds dotfile groups feature to configuration and CLI.

The PR appears safe to merge, with no new blocking issues found.

What we checked:

• Targeted apply prunes other groups: requests rejects --prune with target arguments before run_inner reaches any writes.
• Refused removal loses its record: remove_recorded keeps the path after a removal error. It only drops paths that were not kept.

Summary

Adds named dotfile groups, machine-specific selection, and saved records for status and removal.

• Groups support directory walks and individual entries.
• add and edit can route files into group sources.
• The latest changes reject target arguments with --prune and repeat Windows removal checks immediately before deletion.
• No new actionable issues were found in the changes since the previous review.

_{Reviews (9) · Last reviewed commit: "fix(dotfiles): recheck links before grou..."}

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Actionable comments posted: 1

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⚠️ Outside diff range comments (1)

🟠 Major · Add group to the allowed keys in validate_incoming_files. · files.rs:951-976

src/system/files.rs:951-976
🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

Add group to the allowed keys in validate_incoming_files.

This PR adds group to file_entry_from_toml and to FileTomlEntry. The key allowlist in validate_incoming_files does not include group. As a result, preflight for incoming shared config rejects every [dotfiles] entry that has group = "..." with the error unknown dotfile key "group". This error blocks history pulls and bootstrap adoption for configs that use the new feature. Add "group" to the allowlist. Also validate the name with validate_group_name.

Proposed fix

                             | "dot_prefix"
                             | "relative"
+                            | "group"
                     ) {

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Review comment at @src/system/files.rs around lines 951 - 976:
Update the dotfile key allowlist in validate_incoming_files to accept "group",
and validate its value with validate_group_name before accepting incoming
entries. Preserve the existing handling of all other keys.

🧹 Nitpick comments (1)

schema/mise.json (1)

6800-6806: 📐 Maintainability & Code Quality | 🔵 Trivial | 💤 Low value

Add the group-name pattern to the bootstrap.dotfile_groups items.

The schema checks group names in dotfile_groups keys and in the entry group field with ^[A-Za-z0-9_.-]+$. The bootstrap.dotfile_groups items do not have this check. If a user writes an invalid name in this list, editor validation accepts it. At runtime, the name only produces an "undeclared" warning. Add the same pattern to the items so that the schema gives the same result in all three places.

Proposed fix

           "items": {
-            "type": "string"
+            "type": "string",
+            "pattern": "^[A-Za-z0-9_.-]+$"
           }

🤖 Prompt for AI Agents

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Review comment at @schema/mise.json around lines 6800 - 6806:
Add the existing group-name pattern to the string items schema for
bootstrap.dotfile_groups, matching the validation used for dotfile_groups keys
and entry group fields.

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Inline comments:
Review comments at @src/cli/dotfiles/unapply.rs:
- Around line 186-187: Update the recorded-removal loop in `unapply` to exclude
targets claimed by any different active request before calling
`remove_recorded`. Preserve removal of unclaimed targets and targets owned
solely by the request being unapplied.

---

Outside diff comments:
Review comments at @src/system/files.rs:
- Around line 951-976: Update the dotfile key allowlist in
validate_incoming_files to accept "group", and validate its value with
validate_group_name before accepting incoming entries. Preserve the existing
handling of all other keys.

---

Nitpick comments:
Review comments at @schema/mise.json:
- Around line 6800-6806: Add the existing group-name pattern to the string items
schema for bootstrap.dotfile_groups, matching the validation used for
dotfile_groups keys and entry group fields.

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📒 Files selected for processing (31)

• docs/bootstrap.md
• docs/cli/bootstrap/dotfiles/add.md
• docs/cli/bootstrap/dotfiles/apply.md
• docs/cli/bootstrap/dotfiles/edit.md
• docs/cli/bootstrap/dotfiles/status.md
• docs/cli/bootstrap/dotfiles/unapply.md
• docs/cli/dotfiles/add.md
• docs/cli/dotfiles/apply.md
• docs/cli/dotfiles/edit.md
• docs/cli/dotfiles/status.md
• docs/cli/dotfiles/unapply.md
• docs/dotfiles.md
• e2e/cli/test_dotfiles_groups
• e2e/cli/test_dotfiles_groups_ownership
• man/man1/mise.1
• mise.usage.kdl
• schema/mise.json
• src/cli/dotfiles/add.rs
• src/cli/dotfiles/apply.rs
• src/cli/dotfiles/edit.rs
• src/cli/dotfiles/mod.rs
• src/cli/dotfiles/status.rs
• src/cli/dotfiles/track.rs
• src/cli/dotfiles/unapply.rs
• src/config/config_file/mise_toml.rs
• src/config/config_file/mod.rs
• src/oci/builder.rs
• src/system/dotfile_groups.rs
• src/system/files.rs
• src/system/history/tracked.rs
• src/system/mod.rs

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Actionable comments posted: 1

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Inline comments:
Review comments at @src/system/dotfile_groups.rs:
- Around line 647-664: Update the retain condition in the group record path
around `record.paths.retain` so an old safe-to-remove path under a requested
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• src/system/dotfile_groups.rs
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Inline comments:
Review comments at @src/system/dotfile_groups.rs:
- Around line 980-997: Update the starting-directory open in remove_no_follow so
O_NOFOLLOW is omitted when start is the parent of a single-file root, allowing a
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- Line 817: Update the pruning flow around group_requests and orphaned to track
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Instruction counts

benchmark	trend	instructions	Δ	wall (min)	Δ
env	▃▅▄▁▁▁▂█▄▆▄█▃▃▄▄▃▇	27,169,565 → 27,189,694	+0.07%	18.50 → 19.01ms	+2.73%
hook-env	▃▃▄▅▁▂▂▃▄▄▂▄▂▅▅▇▄█	29,111,283 → 29,151,187	+0.14%	19.03 → 19.65ms	+3.23%
ls	▆▆▅▁▄▂▄▆██▆▆▅▇▆▆▆▆	30,636,143 → 30,635,421	-0.00%	20.27 → 20.86ms	+2.87%
registry	▅▅▆▅▆▆▁▂▇▇▇▇▇██▇▇▃	40,112,643 → 40,023,346	-0.22%	17.30 → 17.37ms	+0.43%
startup	▅▆▆▆█▆▆█▁▂▁▂▂▂▇██▇	10,856,598 → 10,852,979	-0.03%	11.56 → 11.69ms	+1.10%

No instruction-count regression above 1%.

_{Only instruction counts gate. Wall clock is shown for context — on identical hardware it moves 4-20% run to run.}

_{Measured by tak — instruction-counted CLI benchmarks, stored in this repository's git notes.}

_{3d316557b541 vs 43405dfb7c2b · measured on the runner, not pushed to the history.}