feat(skills): support root-level SKILL.md single-skill repos

[christso]

Summary

• Add detection for plugins with SKILL.md at the repo root (the default npx skills init layout)
• Read skill name from SKILL.md YAML frontmatter name field, falling back to directory name
• Extend copySkills() in transform.ts to handle flat and root-level layouts (not just skills/ dir)
• Priority: skills/ directory > flat subdirs with SKILL.md > root-level SKILL.md

Closes #243

Test plan

• Unit tests added for root-level SKILL.md discovery (3 new tests)
• All existing tests pass (963 pass, 0 fail)

E2E verification

bun run build

# Create a minimal root-level SKILL.md repo
mkdir /tmp/single-skill-repo
printf '---\nname: my-skill\ndescription: test\n---\n# My skill' > /tmp/single-skill-repo/SKILL.md

# Set up a test workspace
mkdir -p /tmp/test-ws/.allagents
cat > /tmp/test-ws/.allagents/workspace.yaml <<YAML
plugins:
  - /tmp/single-skill-repo
clients:
  - claude
YAML

# Verify skill discovery
cd /tmp/test-ws && /path/to/dist/index.js skills list
# Expected: shows "my-skill" from the installed plugin

# Verify sync copies the SKILL.md
cd /tmp/test-ws && /path/to/dist/index.js workspace sync
ls .claude/skills/my-skill/SKILL.md
# Expected: SKILL.md exists

# Cleanup
rm -rf /tmp/single-skill-repo /tmp/test-ws

🤖 Generated with Claude Code

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