fix(skill_view): exclude skill-internal subdirs from Strategy 3 legacy file matching

[111-test-111]

Problem

Strategy 3 in uses to find legacy flat files anywhere under the skills directory. This incorrectly matches files inside skill-internal subdirectories like references/, templates/, scripts/, assets/.

Real-world example: A user has both:

• mcp/native-mcp/SKILL.md — a standalone MCP skill
• autonomous-ai-agents/hermes-agent/references/native-mcp.md — a reference doc inside the hermes-agent skill

Calling skill_view("native-mcp") finds both via Strategy 3's rglob and throws an Ambiguous skill name error, even though the reference doc is clearly not a standalone skill.

Fix

Add a check in Strategy 3 to skip any file whose path contains a skill-internal subdirectory component (references, templates, scripts, assets). These directories are reserved for supporting documents within existing skills and should never contain standalone legacy skills.

Tests

• Regression test reproducing the exact native-mcp collision scenario
• Parametrized test covering all four excluded subdirectory names
• All 11 collision detection tests pass

[alt-glitch]

Related to the #35743 skill_view collision cluster — same root cause (Strategy 3 rglob matching .md files inside other skills' references//templates//scripts//assets/ dirs). Overlaps open fix PRs #35768 and #27915. Consolidating approaches.

[teknium1]

Thanks for the focused regression report and tests. This is already implemented on current main by a broader follow-up to the skill-view collision cluster noted in the discussion.

• Automated hermes-sweeper review verified that tools/skills_tool.py:1172-1180 excludes support documents from Strategy 3 legacy-file candidate matching.
• The shared predicate in agent/skill_utils.py:73-97 distinguishes actual skill support directories from valid top-level categories named scripts, templates, assets, or references.
• Commit 9137b86a5286e4ea420e9fb894bce34fee546b3d (fix(skills): ignore support docs in skill discovery) shipped this behavior and is included in v2026.6.19.
• Current regression coverage at tests/tools/test_skills_tool.py:1240-1261 verifies that a nested reference document does not collide with a real skill.