agents pull deletes central skill files when agent skills dir is a symlink

[muqsitnawaz]

Bug

agents pull deletes all files from the central ~/.agents/skills/ directory on every run.

Root Cause

When an agent's version-specific skills directory is a symlink to the central ~/.agents/skills/ directory (e.g. Gemini's skills -> ~/.agents/skills), the syncResourcesToVersion function in src/lib/versions.ts follows the symlink and destroys the source files.

The problematic code path (around line 1306):

for (const skill of skillsToSync) {
  const srcDir = path.join(centralSkills, skill);   // ~/.agents/skills/linear
  if (!fs.existsSync(srcDir)) continue;

  const destDir = path.join(skillsTarget, skill);   // symlink -> ~/.agents/skills/linear (SAME directory!)
  removePath(destDir);   // deletes the CENTRAL copy through the symlink
  copyDir(srcDir, destDir);  // srcDir is now gone, copies nothing
  syncedSkills.push(skill);
}

Sequence:

1. removePath(destDir) resolves the symlink and deletes ~/.agents/skills/{skill}/ (the central copy)
2. copyDir(srcDir, destDir) tries to copy from central — but it was just deleted
3. Result: empty skill directories in both central and the version home

This affects every skill on every agents pull invocation. The files are git-tracked so they show up as unstaged deletions (git status shows D skills/*/SKILL.md etc.), and the next pull would auto-commit these deletions via the git add -A in pullRepo.

Reproduction

1. Have a Gemini version installed where skills/ is a symlink to central
2. Run agents pull -y
3. Check ~/.agents/skills/ — all SKILL.md and script files are gone
4. git status in ~/.agents/ shows all skill files as deleted

Suggested Fix

In syncResourcesToVersion, before processing skills, check if the target skills directory (or individual skill subdirectory) is a symlink that resolves to the central source. If so, either:

• Skip the sync (it's already pointing at the source — no copy needed)
• Replace the symlink with a real copy before doing the remove+copy cycle

Something like:

const destDir = path.join(skillsTarget, skill);
const srcDir = path.join(centralSkills, skill);

// If dest is (inside) a symlink to source, skip — already in sync
if (fs.lstatSync(skillsTarget).isSymbolicLink()) {
  const resolved = fs.realpathSync(skillsTarget);
  if (resolved === fs.realpathSync(centralSkills)) {
    continue; // symlinked to source, nothing to do
  }
}

removePath(destDir);
copyDir(srcDir, destDir);

Or more defensively, check at the parent level before entering the loop:

if (fs.lstatSync(skillsTarget).isSymbolicLink()) {
  // Skills dir is a symlink — don't sync, it already points to central
} else {
  // ... existing sync loop
}

Impact

• All skill files (SKILL.md, scripts, reference data) deleted from central on every pull
• Skills stop working until manually restored (git checkout -- skills/)
• If not caught, the next pullRepo auto-commits the deletions, making them permanent