Investigate colin clean cache clearing options

[jlowin]

Context

When renaming a model file (e.g., skill.md → SKILL.md), the cache doesn't invalidate properly because the manifest keys by file path. Running colin run fails with dependency errors until you use --no-cache.

Currently, there's no easy way to clear the cache without:

• rm -rf .colin/ (nuclear)
• rm .colin/manifest.json (forces full recompile)
• colin run --no-cache (ignores cache but doesn't delete it)

colin clean --all only removes stale files, not the entire cache.

Suggestion

Consider adding cache-clearing options to colin clean:

colin clean --cache    # Clear .colin/compiled/ and manifest
colin clean --all      # Everything (output + cache)

Or investigate whether file renames should auto-invalidate cache entries.

Related

There may have been a previous discussion about positional arguments for colin clean - worth checking if this was considered.