fix: properly resolve symlinked directories in scanner

[trevorh]

Summary

• Fixes symlink handling in scanDirectoryWithSkillMd and scanFlatMd — instead of treating all symlinks as directories, now resolves the symlink target with statSync to verify it actually points to a directory
• Adds missing readdirSync import to tool-configs.ts
• Extracts repeated join(baseDir, entry.name) into fullPath variable for clarity

Context

The current code does entry.isDirectory() || entry.isSymbolicLink() which incorrectly treats symlinks to files as directories. This fix uses statSync(fullPath, { throwIfNoEntry: false })?.isDirectory() to properly check the symlink target.

Test plan

• Create a symlink pointing to a file inside a skill directory — verify it's skipped (not treated as a subdirectory)
• Create a symlink pointing to a directory containing skills — verify skills are discovered
• Verify normal (non-symlinked) skill directories still scan correctly

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