[jdx]

https://entire.io/gh/jdx/mise/trails/58

Tracking an individual file inside a private directory did not record the directory's mode, so a fresh machine recreated the directory world-readable. With this configuration and ~/.claude at 0700:

[dotfiles]
"~/.claude/settings.json" = { mode = "track" }

the history manifest recorded nothing about ~/.claude, and mise bootstrap --from-git on a new machine created it with the default 0755 via create_dir_all:

// before
"permissions": {}

Directory modes were only captured for directories that were themselves [dotfiles] entries (and their subdirectories). Reported in #13410 (item 3).

What changes

A checkpoint now records the non-default (not 0755) mode of every directory strictly between a tracked path and the root it is mapped under (home or the mise configuration directory). The same rule applies to file and directory entries, so a tracked ~/.config/nvim inside a 0700 ~/.config records ~/.config too.

// after
"permissions": {
  "home/.claude": 448
}

A containing directory is one filesystem object, so it gets one record under the variant-less path whatever streams the files inside it belong to: ~/.claude/settings.json without variants and ~/.claude/notes with variants = [{ os = "linux" }] share the single home/.claude record, and a save from either stream replaces it. The record applies even when every file inside the directory is platform-specific, so the tree only holds it under a stream such as home@linux/.claude. A directory that is itself an enrolled entry keeps its own per-stream record (home@linux/.claude), as before; when the directory is enrolled here, that stream's record decides its mode and its absence means the default, so another platform's containing record for the same directory does not apply (an enrolled stream the incoming manifest dropped means a machine with that stream saved the directory at the default). A stream marker lives only in the first path component, so a directory whose own name contains @ is an ordinary directory.

On pull and on a fresh bootstrap --from-git, the directory is created (or corrected) with the recorded mode before its files are written. When the directory goes back to 0755 at home, the next save drops the record and the next pull on the other machine restores the default. A machine whose directory already has the incoming mode pulls without saving first, even if its own manifest predates this change and records nothing for it; only a live mode that differs from the incoming one is checked against the local record. That check has one purpose: never overwrite a live mode the user has not saved. The baseline it compares the live mode with is the mode this planner would have applied from the saved manifest: the same computation that decides the incoming mode (the enrolled stream's record covering the directory, absent meaning the default; else the containing record, absent meaning the default), run against the saved manifest with this machine's variant selection. A directory the saved enrollment does not cover has no baseline, and a directory that does not exist live has nothing to guard. Because what a pull applies and what the next pull assumes are one definition, a mode this planner set is never reported back as an unsaved change, tree presence plays no part in the baseline, and a nested enrollment for another platform cannot hide the enclosing enrollment that governs the directory here. The same governing key decides whether a directory step exists at all, in three ways: a file or link at that key in the incoming tree means the path is never turned into a directory because another stream holds one there; a directory at that key means present; and nothing at that key (every file inside lives in a nested variant stream) falls through to the containing rule, where the directory is present when some stream of a path inside it holds it as a directory and none holds something else there. A checkpoint records a directory's mode only from the record under its governing key, so another platform's containing record does not become this machine's rollback target when its own stream records the default. The checkpoint record's tree.modes includes these directories too, so history rollback recreates them privately and an unchanged tree still deduplicates on automatic captures.

A selective save of one child of a manual (autosave = false) directory now records the live mode of every directory the save observed (the manual directory itself, its subdirectories, its parents) while unnamed sibling files keep their saved modes; previously the directory's own mode was stripped as an unnamed sibling and only put back from the previous checkpoint, which could not distinguish an unchanged mode from a stale one.

Deliberately still not recorded

• Home itself and the mise configuration directory itself. Enrolling a file must not capture metadata about your home or a custom configuration root, and a fresh machine's home keeps its own mode.
• Directories whose mode is the default 0755, as before.
• For a path outside every root (not under home or the configuration directory), only the explicitly enrolled directory and its subdirectories, as before.
• A per-stream record for a containing directory (home@linux/.claude): the manifest validator rejects it, and a sibling, the root, or a directory containing no enrolled path is rejected as before.

Known follow-up (pre-existing)

Directory permission steps run before the file steps of the same pull, both on main (for enrolled directories) and here (now also for containing directories). A recorded non-writable mode such as 0555 is therefore applied before files are written into that directory, and the writes fail with permission denied. That ordering is unchanged by this PR; a contained fix (apply desired | 0o700 before the file steps and desired after, with the temporary mode covered by rollback and concurrent-change validation) is left for a follow-up.

Known limitation (not changed here)

A containing directory has one variant-less record. Two machines that keep the same shared parent at different modes, say ~/.claude at 0700 on Linux and 0750 on macOS, overwrite each other's home/.claude record on each save, and each pull applies the other's mode. Nothing is lost or aborted (the unsaved-mode guard still reports a change made after the local machine's last save), but a per-platform mode for a shared containing directory cannot be expressed. Two directions are possible and the choice is the maintainer's: record a containing directory per stream when the files under it are platform-specific, or keep the single record and document last-writer-wins.

Validation

• Unit: cargo test --bin mise history:: (186 passed). New cases cover: a file entry under a 0700 parent records the parent and never home, and the configuration root is its own boundary (checkpoint.rs); capture, replacement on return to default (including a directory named with @), one record across streams, and an inactive directory enrollment for another platform not hiding the parent record (manifest.rs); eligibility of containing directories, one step per directory when an enrolled stream and a containing record name the same directory (with the enrolled stream authoritative even when only the local head records it), a parent present only under a variant stream being planned on a fresh machine and still guarding an unsaved local chmod, a superseded containing key still guarding an unsaved local chmod, a dropped enrolled record read as the default rather than another platform's containing record, a directory newly enrolled in a stream where only a child was enrolled keeping its containing baseline, the inverse (a variant enrollment reduced to a containing record) keeping the record under the selected variant, a new private subdirectory inside an enrolled directory being created rather than guarded, a nested enrollment for another platform not hiding the enclosing enrollment's baseline, adoption and the next pull agreeing on the baseline (a containing change after adopting is planned or needs nothing, never a conflict), a path that is a file in its governing stream getting no directory step even though another stream holds a directory there, a covered directory that exists only in an inner variant stream still getting its recorded mode on a fresh machine, and a matching parent with no local record not being treated as unsaved (sync/directories.rs); parent modes reaching the checkpoint record with deduplication, a checkpoint taking a directory's mode only from its governing stream (shadow.rs), and a selective save of a manual directory's child neither carrying a stale parent mode nor dropping the directory's unchanged mode (checkpoint.rs). Each fix was checked by reverting it and watching its test fail.
• E2E: e2e/cli/test_dotfiles_directory_permissions now tracks ~/.claude/settings.json under a 0700 ~/.claude and a ~/.variant-private/settings.json declared with --os under a 0700 ~/.variant-private; asserts the manifest records home/.claude and home/.variant-private as 448, nothing for home or the per-stream path, and the file under home@<os>/; adopts on a second HOME and asserts both directories come back 0700 while that HOME stays 0755; then chmods ~/.claude back to 0755, saves, and asserts the pull on the second machine follows. test_dotfiles_portable_permissions, test_dotfiles_rollback_types, test_dotfiles_history_policies, test_dotfiles_capture_omissions, and test_dotfiles_files pass as well.
• cargo clippy --bin mise --all-features --all-targets -- -D warnings and mise run lint-fix are clean.

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---

Note

Medium Risk
Changes Unix directory permission capture, sync, and pull conflict detection for dotfiles history—security-sensitive—but behavior is heavily specified and covered by new unit and E2E tests.

Overview
Dotfiles history now persists and restores non-default modes for parent directories of tracked files (e.g. 0700 on ~/.claude when only settings.json is enrolled), so bootstrap/pull no longer recreate those paths as world-readable 0755.

Capture walks ancestors up to—but not including—home or the mise config root via mode_ancestors / updated file_modes, writes a single variant-less manifest key for shared containing dirs (with validation in manifest.rs), and keeps live observed modes on selective manual saves instead of stale carried modes. governing_key / mode_from unify how desired modes are chosen across checkpoint metadata, rollback (shadow.rs), and the rewritten directory pull planner (sync/directories.rs): enrolled-stream records win over cross-platform containing records, tree presence avoids turning files into directories, and unsaved local chmods are gated against the same baseline the last saved manifest would have applied.

Docs (history.md) and e2e/cli/test_dotfiles_directory_permissions cover ~/.claude and OS-variant parents; extensive unit tests were added for variant/enrollment edge cases.

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📝 Walkthrough

Walkthrough

The change records non-default directory permissions below tracked roots, resolves permission ownership across variants, and applies those permissions during synchronization. Tests cover private parents, stale-mode handling, fresh-machine recreation, and propagation to another machine.

Changes

Tracked directory permission metadata

Layer / File(s)	Summary
Capture directory ancestors src/system/history/checkpoint.rs, src/system/history/sync/layout.rs	Checkpoint capture records non-default directory ancestors below applicable roots. Live directory modes take precedence over carried saved modes.
Record and validate permission ownership src/system/history/manifest.rs, src/system/history/shadow.rs	The manifest resolves governing enrollment keys. Tree metadata records containing directories once without variants.
Apply eligible directory modes src/system/history/sync/directories.rs	Directory synchronization distinguishes enrolled and containing claims, resolves variant candidates, creates missing directories, emits one step per directory, and checks unsaved local modes.
Validate private directory behavior e2e/cli/test_dotfiles_directory_permissions, docs/history.md	End-to-end coverage and documentation describe private directory capture, recreation, mode changes, root exclusion, and synchronization.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~45 minutes

Change: Bug fix

Sequence Diagram(s)

sequenceDiagram
  participant Checkpoint as checkpoint.rs
  participant Manifest as manifest.rs
  participant DirectorySync as sync/directories.rs
  participant Filesystem
  Checkpoint->>Filesystem: inspect tracked file and directory modes
  Checkpoint->>Manifest: store containing directory modes
  DirectorySync->>Manifest: resolve governing enrollment and permission baseline
  DirectorySync->>Filesystem: apply one permission step per directory

Loading

Merge Risk: 🟡 Moderate · up to 551b0

Directory synchronization can overwrite unsaved permission changes, select an unsafe default mode, or fail while applying tracked files under restrictive directories. Resolve these synchronization risks before merging.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 76.74% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 43 functions across 5 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

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Check name	Status	Explanation
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 describes the primary change: recording permission modes for directories that contain tracked files. It is concise and directly related to the pull request.

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🟠 Major · Preserve ancestor modes for held files. · checkpoint.rs:291-324

src/system/history/checkpoint.rs:291-324
🗄️ Data Integrity & Integration | 🟠 Major | ⚡ Quick win

Preserve ancestor modes for held files.

When a held tracked file’s parent changes to a non-default mode, file_modes records that ancestor because the held file remains in walk.files. The held-mode block restores only the exact held path. hold_paths later restores the held content, but manifest.capture_permissions still persists the changed ancestor mode, so a checkpoint before the file is due can carry that mode forward.

Filter ancestors observed only through held files, or restore their previous mode (or absence). If an unheld tracked file also observes the directory, keep the live mode.

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In `@src/system/history/checkpoint.rs` around lines 291 - 324, Update the
held-mode handling around file_modes and the draft.held loop so ancestor modes
observed only through held tracked files are restored from
previous_checkpoint.tree.modes, or removed when previously absent; retain the
live mode whenever an unheld tracked file also observes that ancestor. Ensure
held-path restoration continues to preserve the existing exact-path behavior.

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Outside diff comments:
In `@src/system/history/checkpoint.rs`:
- Around line 291-324: Update the held-mode handling around file_modes and the
draft.held loop so ancestor modes observed only through held tracked files are
restored from previous_checkpoint.tree.modes, or removed when previously absent;
retain the live mode whenever an unheld tracked file also observes that
ancestor. Ensure held-path restoration continues to preserve the existing
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• src/system/history/sync/layout.rs

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Confidence Score: 5/5

The PR appears safe to merge, with the previous findings addressed and no new blocking defects identified.

Summary

Records non-default permissions for directories containing tracked files, preserving private parent directories during bootstrap, pull, and rollback without recording home or configuration-root permissions.

• Shares containing-directory records across streams while preserving enrolled-stream precedence.
• Uses one governing-key calculation for incoming modes, saved baselines, and checkpoint reconstruction.
• Checks object types in the governing stream and retains fallback support for directories represented only in nested streams.
• Adds regression coverage for selective saves, mixed-stream types, permission restoration, and bootstrap.
• The previous findings are addressed; no additional actionable issues were established in the changes since the previous review.

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Inline comments:
In `@src/system/history/sync/directories.rs`:
- Around line 102-114: Update the claim selection around the claimed entry so
candidates with a corresponding incoming record in tracked.manifest.permissions
outrank candidates without one, then use the existing claim rank as the
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applies the incoming mode, including private modes, instead of falling back to
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🟠 Major · Do not apply a non-writable final mode before file synchronization. · directories.rs:225

src/system/history/sync/directories.rs:225
🩺 Stability & Availability | 🟠 Major | 🏗️ Heavy lift

Do not apply a non-writable final mode before file synchronization.

A recorded mode such as 0o555 is valid and can contain readable tracked files on the source machine. On a fresh machine, this line removes owner write permission before synchronization writes those files. File creation or atomic replacement then fails with PermissionDenied.

Populate the directory with a temporary owner-only writable mode, such as desired | 0o700. Apply desired after file synchronization completes. Include the temporary mode in rollback and concurrent-change validation.

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In `@src/system/history/sync/directories.rs` at line 225, Update the directory
synchronization flow around set_mode to apply a temporary owner-writable mode
(desired combined with 0o700) before files are created or replaced, then apply
desired only after synchronization completes. Track the temporary mode in
rollback and concurrent-change validation so failures restore and verify the
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Inline comments:
In `@src/system/history/sync/directories.rs`:
- Around line 166-185: The saved_bits calculation must preserve the 0o755
baseline when a previously enrolled variant directory becomes a variant-less
containing directory and its permission record is absent. Update the enrollment
lookup around claim and a_newly_enrolled_parent_keeps_its_containing_baseline to
derive the baseline from saved enrollment ownership, including the selected
variant, and add the inverse regression coverage for an unsaved live-mode
change.

---

Outside diff comments:
In `@src/system/history/sync/directories.rs`:
- Line 225: Update the directory synchronization flow around set_mode to apply a
temporary owner-writable mode (desired combined with 0o700) before files are
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Instruction counts

Nothing was compared, and so nothing was gated. No series appears on both sides: either the base has no measurements recorded, or the two were measured on different runner classes, which are deliberately not comparable — counts shift between machine types by more than a real regression does.

New, nothing to compare against: env on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143, hook-env on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143, ls on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143, registry on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143, startup on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143

_{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.}

_{309250b5125e vs c267eaff1b39 · measured on the runner, not pushed to the history.}