fix(skill): support standalone skill URLs

[christso]

Summary

• honor GitHub subpaths when installing, listing, and bulk-enabling direct skill sources
• recognize subpath basenames as valid plugin aliases so follow-up skill operations work
• make git cloning more tolerant for large standalone skill repos and skip invalid cached subpaths during sync

E2E

Red

cd /tmp/<workspace>
HOME=/tmp/<home> node /home/entity/projects/EntityProcess/allagents.worktrees/feat-standalone-skills/dist/index.js skill add https://github.com/NousResearch/hermes-agent/tree/main/skills/research/llm-wiki

Observed before fix: Skill 'llm-wiki' not found in plugin ..., and the clone path could also time out on this large repo.

Green

cd /tmp/<workspace>
HOME=/tmp/<home> node /home/entity/projects/EntityProcess/allagents.worktrees/feat-standalone-skills/dist/index.js skill add https://github.com/NousResearch/hermes-agent/tree/main/skills/research/llm-wiki

Verified after fix:

• command reports Enabled skill: llm-wiki (llm-wiki)
• .allagents/workspace.yaml stores the source URL with skills: [llm-wiki]
• .agents/skills/llm-wiki/SKILL.md exists

Validation

bun run lint
bun run typecheck
bun test
bun run build

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