Support marketing/{skills,squads} project layout and ignore non-run output directories in runs

[canovars]

Summary

The current CLI assumes that project-level skills and squads always live at the repository root:

• skills/
• squads/

That breaks projects organized by department, where the canonical layout is:

• marketing/skills/
• marketing/squads/

There is also a second issue in runs: it treats any directory under output/ as a run, which causes false positives for asset folders such as output/images/ and output/slides/.

Current behavior

• npx opensquad skills only reads skills/
• npx opensquad runs <squad> only reads squads/
• npx opensquad runs <squad> treats any folder in output/ as a run id

Expected behavior

• Prefer marketing/skills/ when it exists, with fallback to skills/
• Prefer marketing/squads/ when it exists, with fallback to squads/
• Only treat real run directories as runs, for example YYYY-MM-DD-HHmmss and YYYY-MM-DD-HHmmss-N

Minimal reproduction

1. Create a project using:
   • marketing/skills/example-skill/SKILL.md
   • marketing/squads/example-squad/output/images/
   • marketing/squads/example-squad/output/slides/
2. Run npx opensquad skills
3. Run npx opensquad runs example-squad

Observed today:

• skills does not find example-skill
• runs does not resolve the squad path unless the project also keeps a legacy squads/ alias
• when the squad path is resolved, images and slides can be reported as if they were runs

Environment

• OS: macOS Darwin 25.4.0
• Node.js: v24.11.1
• npm: 11.6.2
• IDE: Codex / Claude Code-compatible local environment

Proposed fix

Keep the upstream change minimal and runtime-only:

• update src/skills.js to resolve marketing/skills/ first, then fallback to skills/
• update src/runs.js to resolve marketing/squads/ first, then fallback to squads/
• update src/runs.js to ignore non-run directories inside output/

I already prepared a patch for opensquad@0.1.15 plus matching tests for skills and runs.

Notes

• This preserves backward compatibility for existing root-based projects.
• I intentionally did not include template or documentation changes in the patch, to keep the proposal narrowly scoped to CLI/runtime behavior first.
• I checked the current upstream master branch before preparing this report: src/skills.js still resolves only skills/, and src/runs.js still resolves only squads/ and lists every output/ subdirectory as a run.

[canovars]

Opened PR #24 for this fix: #24