Windows: ruler apply can fail with EPERM during native skills rename

[BartNetJS]

Summary

ruler apply on Windows can fail during native skills propagation with:

[ruler] EPERM: operation not permitted, rename '...\\skills.tmp-<timestamp>' -> '...\\skills'

This reproduces on @intellectronica/ruler@0.3.38, which is also the latest npm version at the time of testing.

Reproduction

Project root contained a .ruler/skills directory and native agent folders including .claude.

Command:

ruler apply

Observed failure:

[ruler] Nested mode is experimental and may change in future releases.
[ruler] Skills are configured, but the following agents do not support native skills and will be skipped: Warp
[ruler] Skills support is experimental and behavior may change in future releases.
[ruler] EPERM: operation not permitted, rename 'C:\Users\...\Atlas\\.claude\\skills.tmp-1775568298919' -> 'C:\Users\...\Atlas\\.claude\\skills'

Isolation

ruler apply --skills false completes successfully, so the failure is isolated to the native skills propagation step.

The installed CLI implementation uses a direct fs.rename(tempDir, targetDir) after copying .ruler/skills to a temporary directory. On Windows this can lose a race with Defender or another filesystem lock and return EPERM.

Root cause

In the current release, skills propagation uses a direct rename with no retry and no fallback copy path.

Affected implementation area:

• dist/core/SkillsProcessor.js
• propagateSkillsForClaude
• propagateSkillsForCodex
• propagateSkillsForOpenCode
• equivalent functions for other native-skills targets

Workarounds verified locally

1. ruler apply --skills false succeeds.
2. A local patch that wraps the final replace step with:
   • retry on EPERM, EBUSY, and ENOTEMPTY
   • fallback to copy-and-remove when rename still fails

After that local patch, plain ruler apply succeeded.

Suggested fix

In SkillsProcessor, replace the direct fs.rename(tempDir, targetDir) with a helper that:

1. retries transient Windows rename errors
2. falls back to copy-and-remove if the rename keeps failing
3. keeps temp-directory cleanup in the existing error path

That should preserve the current behavior on normal filesystems while making skills propagation reliable on Windows.