fix(core): dedupe symlinked/junctioned skills directories during discovery

[aniruddhaadak80]

Summary

Fixes #28944

When a user links their .gemini folder to .agents (Windows junction via \mklink /J .gemini .agents, or a symlink) to follow the open Agent Skills standard while retaining compatibility, the CLI scanned both configured entry points (.gemini/skills and .agents/skills) as if they were separate directories. Since discovery did not resolve aliases to their physical paths, identical skills were registered twice, producing duplicate-skill conflict warnings on every startup and /skills reload.

Changes

• \SkillManager.discoverSkills\ now tracks scanned directories by their physical (real) path (\s.realpath) and skips any directory that resolves to an already-scanned location.
• Applies to both tiers where the alias exists: user-level (~/.gemini/skills\ / ~/.agents/skills) and workspace-level (<ws>/.gemini/skills\ / <ws>/.agents/skills). Built-in and extension skills are unaffected.
• Non-existent directories fall back to their resolved path, preserving existing behavior.

Behavior after the fix

With .gemini -> .agents: skills are discovered exactly once from the first entry point; no \Skill conflict detected: ... overriding ...\ warnings. With two genuinely distinct directories, behavior is unchanged (including existing alias precedence).

Testing

• Added end-to-end tests in \skillManagerAlias.test.ts:
  • Workspace tier: .agents/skills/my-skill/SKILL.md\ with .gemini\ created as a real junction/symlink → skill discovered once, zero conflict warnings (skips gracefully on platforms that disallow directory links).
  • User tier: same scenario for ~/.gemini -> ~/.agents.
• Full \src/skills\ suite passes (29 tests), plus eslint, prettier, and \ sc --noEmit\ on @google/gemini-cli-core.

Documentation

• I have updated the documentation accordingly (N/A — no user-facing docs describe this internal dedupe; behavior now matches the expectations in /skills reload reports duplicate warnings when .gemini is symlinked/junctioned to .agents #28944).

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses an issue where identical skills were being registered multiple times when users employed symlinks or Windows junctions to alias their skill directories. By resolving paths to their physical locations during the discovery process, the system now correctly identifies and skips redundant scans, eliminating unnecessary conflict warnings and improving startup performance.

Highlights

• Deduplication of Skill Directories: Implemented a mechanism in SkillManager to track scanned directories by their physical path, preventing duplicate skill discovery when symlinks or junctions are used.
• Improved Path Resolution: Added a new private method 'loadSkillsFromUniqueDir' that resolves paths to their real locations before scanning, ensuring consistent behavior across aliased directories.
• Regression Testing: Added comprehensive end-to-end tests in 'skillManagerAlias.test.ts' to verify that linked directories are scanned exactly once and do not trigger conflict warnings.

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[github-actions]

📊 PR Size: size/M

• Lines changed: 162
• Additions: +158
• Deletions: -4
• Files changed: 2

[gemini-code-assist]

Code Review

This pull request introduces a mechanism to prevent duplicate skill discovery when directories are symlinked or junctioned (e.g., .gemini pointing to .agents). It adds a loadSkillsFromUniqueDir helper in SkillManager that resolves directories to their physical paths using fs.realpath and tracks visited paths in a Set. Additionally, corresponding unit tests are added to verify that duplicate skills are not reported under symlinked/junctioned alias directories. There are no review comments, so I have no feedback to provide.

[gemini-cli]

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