[jdx]

https://entire.io/gh/jdx/mise/trails/133

When mise writes a dotfile into a directory that does not exist yet, it creates the missing parents. Until now those directories stayed behind after mise removed the file, so a work-only config like ~/.config/newapp/sub/work.toml left an empty ~/.config/newapp/sub/ tree once it was switched off or unapplied. This addresses the "remove directories left empty" part of #13410.

mise now records the parent directories it creates for a single-file target, and removes them with the target once they are empty:

[dotfiles]
"~/.config/newapp/sub/work.toml" = { source = "work.toml.tera", mode = "template", remove_empty = true }

With ~/.config present and ~/.config/newapp absent:

$ WORK=1 mise dot apply --yes     # creates newapp/ and newapp/sub/, writes work.toml
$ mise dot apply --yes            # WORK unset: the template renders empty
mise files: removed ~/.config/newapp/sub/work.toml (template rendered empty)

work.toml, newapp/sub/, and newapp/ are gone; ~/.config stays.

The same applies to mise dot unapply for symlink, copy (single file), template, and inline content entries, and --dry-run lists the directories it may remove:

$ mise dot unapply --dry-run
rm ~/.config/copyapp/deep/copied
rmdir ~/.config/copyapp/deep (if empty)
rmdir ~/.config/copyapp (if empty)

What is kept

The walk goes upward from the target's parent and stops at the first directory that fails any of these checks:

• mise created it. Directories that already existed when mise first wrote the target (~/.config above) are never removed.
• It is empty. A directory holding anything else, such as a file you added next to the target, stays, and so does everything above it.
• No other entry needs it. A directory that is another active entry's target, or one a symlink-each or directory copy entry places files in, stays.
• It is physically inside $HOME. Your home directory, everything above it, and everything outside it are never removed, even if mise created them. A target such as /opt/newapp/app.toml leaves /opt/newapp in place, because directories outside home may be shared with other software. The check resolves symlinks, so with ~/.config -> /opt/config, ~/.config/app is kept too. Symlinked parents still work for apply.

Pruning runs once every target in an apply or unapply is gone. Only the first entry written into a new directory records it, so each walk counts the directories recorded by any target removed in the same run. Two sibling files in a directory mise created therefore take it along, whichever is removed first. Unapplying an entry whose target is already gone still clears its record and removes the recorded directories once they are empty. That covers a file you deleted by hand, and a directory a remove_empty apply kept because it held a file of yours.

Directory removals are journaled like other dotfile changes, so an interrupted operation is recovered. Pruning is best effort. A directory that can't be removed produces a warning and stays recorded, and later applies retry it even though the target is already gone. It is never shown as a file change.

Limits

• The record lives in the per-target ownership state file (from feat(dotfiles): remove a template's target when it renders empty #13515) ($MISE_STATE_DIR/dotfiles/targets/), as a new created_dirs field. Targets written before this change have no such field and remove no directories. A later apply that creates nothing new keeps the directories already recorded.
• mise dot undo restores a removed file and recreates its parents, but not the record. Those directories are then not considered mise's, so a later removal keeps them. This errs toward leaving an empty directory rather than removing one mise cannot prove it created.
• Directory copy and symlink-each entries keep their existing cleanup inside the target and do not record parents above it.
• A mode = "absent" entry (feat(dotfiles): remove targets with mode = "absent" #13513) creates nothing and records nothing. Records are keyed by target path, so when an absent entry removes a file that an earlier copy, symlink, template, or content entry wrote, it prunes that entry's recorded directories the same way. An absent target with no record removes no directories.

The three existing upward walks (symlink-each stale links, symlink-each reconciliation, unapply of directory entries) now share one helper with the new one. Their behavior is unchanged.

Validation

• Unit tests for the walk cover: directories that existed before vs ones mise created, a non-empty directory, a directory missing from the record, one already removed, $HOME and above, targets outside home, a symlinked parent pointing outside home, unapply plans for every single-file kind whose target is gone, sibling targets removed in either order, a directory another entry needs, recording and merging on apply, and journaling a created parent.
• New e2e test test_dotfiles_prune_created_dirs, where each scenario uses its own directory. It covers: a nested template target that renders empty removes newapp/sub and newapp but keeps ~/.config; a parent with an unrelated file stays; the recorded set merges across applies; unapply of an already-removed target prunes its leftover directory; a copy deleted by hand has its created parents and record removed by unapply; a forced removal of an unreadable target prunes its parents; a copy changed to mode = "absent" takes its created parents along; a record without the new field removes nothing; sibling templates are removed together in both orders; unapply of a copy into a fresh nested directory removes the created directories and undo restores them; and a directory another entry needs stays.
• test_dotfiles_template_remove_empty now expects ~/.config/app to go with its target. On the final revision, these pass locally (Linux): test_dotfiles_prune_created_dirs, test_dotfiles_template_remove_empty, test_dotfiles_absent, test_dotfiles_unapply, the system::files unit tests, clippy with --all-features, and mise run lint. The full dotfiles and bootstrap e2e suites passed on an earlier revision.

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Summary by CodeRabbit

• Bug Fixes
  • mise dot now removes empty parent directories it created when managed targets are removed or changed to absent.
  • Cleanup is limited to empty directories inside the home directory; pre-existing directories, paths outside the home directory, and paths through symlinked parents are preserved.
  • Directories containing unrelated files or other managed targets are kept. If cleanup cannot be completed, it can be retried on a later run.

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📝 Walkthrough

Walkthrough

Apply and unapply now record and prune eligible directories created for single-file dotfile targets. Pruning is limited to empty, unclaimed directories inside the physical home directory. Directories that remain are retained for retry.

Changes

Dotfile Created-Directory Pruning

Layer / File(s)	Summary
Record created directories and define pruning src/system/files.rs	Target state records directories created for supported single-file modes. Shared helpers select and remove eligible directories, track active claims, and retain records for directories that remain.
Prune recorded directories during apply src/system/files.rs, e2e/cli/test_dotfiles_prune_created_dirs	Apply prunes after target removals and retries leftover directories on later runs. Tests cover empty renders, absent entries, shared or claimed directories, and retries.
Prune recorded directories during unapply src/system/files.rs, src/cli/dotfiles/unapply.rs, src/system/unapply.rs, e2e/cli/test_dotfiles_prune_created_dirs, e2e/cli/test_dotfiles_template_remove_empty, docs/dotfiles.md	Unapply receives configuration to identify active directory claims and prunes recorded directories after target removal. Tests and documentation cover unapply behavior, pruning boundaries, and directory recreation.

Estimated code review effort: 3 (Moderate) | ~25 minutes

Sequence Diagram(s)

sequenceDiagram
  participant Apply as execute_apply
  participant State as TargetState
  participant Prune as prune_created_dirs
  participant Unapply as execute_unapply
  Apply->>State: Read recorded created directories
  Apply->>Prune: Prune after target removals
  Prune->>State: Remove successfully pruned directories from records
  Unapply->>State: Read and clear target records
  Unapply->>Prune: Prune recorded directories after target removal

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Merge Risk: ⚪ Minimal · up to a03aa

mise now removes empty directories it created for single-file dotfiles when those dotfiles are removed. Directories that existed before, still hold other files, or are needed by another entry are kept, and nothing outside the home directory is touched. A directory that cannot be removed no longer causes apply or unapply to fail; mise retries it on a later apply. No unresolved risk remains, and the change is ready to merge.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	Docstring coverage is 82.69% which is sufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 52 functions across 3 files. (1 skipped: 1 …
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.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the main change: removing directories created by mise after they become empty.

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[greptile-apps]

Confidence Score: 5/5

The PR appears safe to merge; the previous directory-boundary and retry findings are resolved, and no new actionable defect remains.

Summary

This PR records parent directories created for single-file dotfile targets and prunes them after the targets are removed, while preserving pre-existing, non-empty, claimed, and physically out-of-home directories.

• Extends apply and unapply planning to coordinate directory ownership records, journaling, dry-run output, and sibling targets.
• Retries previously unsuccessful pruning when an absent target is otherwise converged.
• Documents the cleanup boundary and adds unit and end-to-end coverage for ownership, symlinks, retries, undo, and shared directories.

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Actionable comments posted: 1

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Inline comments:
In `@src/system/files.rs`:
- Line 3503: Update the prune_created_dirs calls in execute_apply and
execute_unapply so pruning errors are logged as warnings and do not fail the
operation after target changes have been applied. Keep processing subsequent
cleanup and state-recording steps when pruning fails.

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