fix(core): dedupe symlinked skill directories

[neriousy]

Issue for this PR

Closes #17219

Type of change

• Bug fix
• New feature
• Refactor / code improvement
• Documentation

What does this PR do?

Symlinked skill aliases could cause the same physical skill to be discovered multiple times, which produced duplicate skill directory permission rules.

This PR dedupes skills by canonical path while keeping the existing last-discovered alias behavior.

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How did you verify your code works?

Added some tests

You can run the reproduction steps in the issue mentioned earlier

Screenshots / recordings

If this is a UI change, please include a screenshot or recording.

Checklist

• I have tested my changes locally
• I have not included unrelated changes in this PR

If you do not follow this template your PR will be automatically rejected.

[github-actions]

The following comment was made by an LLM, it may be inaccurate:

I found a potentially related PR:

PR #15483: fix: symlink path resolution causing duplicate instances
#15483

This PR appears to address a similar issue - it deals with symlink path resolution causing duplicate instances. While this is a closed/merged PR from earlier, it may be related to the current issue being fixed in PR #17245, particularly around how symlinked paths are being handled to prevent duplicates.

The current PR (#17245) specifically addresses symlinked skill aliases causing duplicate skill discoveries and deduplicates by canonical path. This prior PR seems to have tackled a related symlink duplication problem, so it's worth reviewing to ensure consistency and that the current fix complements or improves upon the previous solution.

[Copilot]

Pull request overview

Fixes duplicate permission rules caused by symlinked skill aliases by deduplicating discovered skill directories using their canonical (real) paths while preserving the existing “later-discovered path wins” behavior.

Changes:

• Deduplicate skill directory paths by canonical/real path during skill discovery, keeping the later-discovered alias path for permissions.
• Add coverage for symlinked skill alias deduping at the skill discovery layer.
• Add coverage ensuring only a single external_directory allow rule is generated for symlinked skill aliases.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
packages/opencode/src/skill/skill.ts	Canonical-path dedupe for skill directories while retaining later-discovered alias path behavior.
packages/opencode/test/skill/skill.test.ts	Adds a regression test asserting symlinked aliases produce a single deduped skill directory entry and that the later path is kept.
packages/opencode/test/agent/agent.test.ts	Adds a regression test asserting only one external_directory allow rule is produced for symlinked skill aliases.

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