What does this PR do?

Fixes skills discovery when a category directory under ~/.hermes/skills/ is a symlink, and makes the main skill scanner paths agree on which SKILL.md files exist.

The root issue was that agent.skill_utils.iter_skill_index_files() had already been fixed to follow symlinks, but tools/skills_tool.py and agent/skill_commands.py still used their own Path.rglob() scans. That left symlinked category trees invisible to skills_list(), skill_view(name=...), and slash-command scanning, while other skill-index code paths could see a different set of files.

This patch moves those remaining scan paths onto the shared symlink-following iterator and makes the skill_view() not-found hint use the same sort order as skills_list().

Related Issue

Fixes #

Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✅ Tests (adding or improving test coverage)

Changes Made

• Switched _find_all_skills() in tools/skills_tool.py from rglob("SKILL.md") to iter_skill_index_files(..., "SKILL.md")
• Switched the name-based skill_view() scan path onto the same iterator so symlinked category directories resolve normally
• Switched agent.skill_commands.scan_skill_commands() onto the same iterator so slash-command scanning matches the main skill index
• Added a shared _sort_skills() helper so skills_list() ordering and the skill_view() available-skills hint stay aligned
• Added regression tests for symlinked category discovery in both the tool and slash-command scanner paths
• Added a regression test covering the skill_view() not-found hint ordering

How to Test

1. Create a category symlink under ~/.hermes/skills/ pointing outside the local tree, with valid SKILL.md skills under the target directory.
2. Verify skills_list() and skills_list(category="...") include the symlinked skills and category.
3. Verify skill_view(name="...") resolves a skill from that symlinked category, and slash-command scanning also sees it.

Checklist

Code

• I've read the Contributing Guide
• My commit messages follow Conventional Commits (fix(scope):, feat(scope):, etc.)
• I searched for existing PRs to make sure this isn't a duplicate
• My PR contains only changes related to this fix/feature (no unrelated commits)
• I've run pytest tests/ -q and all tests pass
• I've added tests for my changes (required for bug fixes, strongly encouraged for features)
• I've tested on my platform: Ubuntu 24.04

Documentation & Housekeeping

• I've updated relevant documentation (README, docs/, docstrings) — or N/A
• I've updated cli-config.yaml.example if I added/changed config keys — or N/A
• I've updated CONTRIBUTING.md or AGENTS.md if I changed architecture or workflows — or N/A
• I've considered cross-platform impact (Windows, macOS) per the compatibility guide — or N/A
• I've updated tool descriptions/schemas if I changed tool behavior — or N/A

Screenshots / Logs

Validation runs:

• source venv/bin/activate && scripts/run_tests.sh -n 4 tests/tools/test_skills_tool.py tests/agent/test_skill_commands.py
  • Passed: 113 passed in 2.18s
• source venv/bin/activate && scripts/run_tests.sh -n 4 tests/agent/test_external_skills.py
  • Passed: 11 passed in 1.01s
• source venv/bin/activate && scripts/run_tests.sh -n 4
  • Repo baseline is currently not green: 41 failed, 14756 passed, 39 skipped, 206 warnings in 310.74s
  • Failures were spread across unrelated areas including gateway approval, DingTalk, Discord bot filter, MiniMax provider switching, provider config validation, backup/profile restoration, tips corpus, several Anthropic-path tests, browser/tool registration, Tirith security, write-deny, and zombie cleanup.