Summary

A user reported that npx allagents plugin uninstall <plugin> printed ✓ Uninstalled plugin (user scope): ... and then crashed with Error: EPERM: operation not permitted, scandir 'C:\$WinREAgent\Scratch\Mount\Windows\System32\LogFiles\WMI\RtBackup'. They were already on v1.13.2 (past the #434 getHomeDir() fix), so this was a different bug.

Root cause: their ~/.allagents/workspace.yaml had a corrupted plugin entry — a bare \ — which resolves to the drive root on Windows. walkForSkillMd (the recursive skill scanner in src/core/skills.ts) had no try/catch and no symlink guard (unlike its sibling discoverRepoSkills in repo-skills.ts), so it recursed unguarded into C:\ and crashed the entire post-uninstall sync — even though the uninstall itself had already succeeded, and even though the bad plugin wasn't the one being uninstalled (sync scans every installed plugin).

• walkForSkillMd hardening (src/core/skills.ts): catches readdir errors and records a warning with remediation steps instead of throwing; skips symlinks/junctions to avoid unbounded recursion through loops. Warnings thread through collectPluginSkills → collectAllSkills/collectAvailableSkillNames → SyncResult.warnings, deduplicated since the same bad plugin gets scanned twice internally.
• Entry-point validation (src/utils/plugin-path.ts, workspace-modify.ts, user-workspace.ts): addPlugin/addUserPlugin now reject a local-path source that resolves to a filesystem root (new isFilesystemRoot helper) — closing the entry point that let the bare \ get written in the first place. There's no legitimate use case for a plugin source that resolves to a drive/filesystem root.
• Fixed a related silent gap: runUserSyncAndPrint (plugin.ts) never printed the Warnings: section at all (unlike its project-scope sibling runSyncAndPrint) — user-scope syncs were silently swallowing every warning, not just the new ones.

Test plan

• bun test — new/extended unit tests in skills.test.ts, plugin-path.test.ts, sync-resilient.test.ts, workspace-modify.test.ts, user-workspace.test.ts all pass
• bun run typecheck and bun run lint clean
• Manual E2E against the built CLI (bun run build, node dist/index.js ...):
  • Temp workspace with a good plugin + a plugin whose resolved path is unreadable (a file standing in for the real bug's drive-root path) → plugin uninstall <good-plugin> --scope user succeeds, sync completes (exit 0), and prints exactly one deduplicated warning with remediation steps instead of crashing.
  • plugin install "\" (both project and user scope) → rejected with Plugin source cannot be a filesystem root directory: \, exit 1, workspace.yaml untouched.