hermes - 💡(How to fix) Fix feat: Allow custom subdirectories in skill linked_files discovery

Problem

skill_manager_tool.py hardcodes ALLOWED_SUBDIRS to only 4 directories:

# Line 171
ALLOWED_SUBDIRS = {"references", "templates", "scripts", "assets"}

Any custom subdirectory is invisible to skill_view — it won't appear in linked_files, so agents can't discover them automatically.

Why this matters

For complex, multi-phase workflows, the recommended pattern is a dispatcher skill + sub-skills structure:

my-workflow/
├── SKILL.md          # Dispatcher: defines phases and routing
├── steps/            # Sub-skills for each phase
│   ├── step-1.md
│   ├── step-2.md
│   ├── step-3.md
│   ├── step-4.md
│   ├── step-5.md
│   └── step-6.md
├── scripts/          # Execution scripts
└── references/       # Documentation

The dispatcher SKILL.md says "load steps/step-1.md for Phase 1", but because steps/ isn't in ALLOWED_SUBDIRS, skill_view never lists those files in linked_files. The agent has to guess file paths from the main SKILL.md text, which is error-prone and breaks the intended routing mechanism.

Suggested fix

Two options:

1. Auto-discover all subdirectories — scan the skill directory and include any subdir containing .md or .py files in linked_files, removing the hardcoded whitelist entirely.

2. Make it configurable — allow skills to declare additional subdirs in frontmatter metadata:

metadata:
  hermes:
    subdirs: [references, scripts, steps]

Option 1 is simpler and more flexible — there's no security reason to restrict subdirectory names (these are local files, not user input).

Workaround

Users can manually patch ALLOWED_SUBDIRS in skill_manager_tool.py, but this breaks on upgrade.