chore: adopt oagen manifest-based stale-file pruning

Track every emitted path in `.oagen-manifest.json` so subsequent
`oagen generate` runs can deterministically delete files that fall out
of the IR, preventing the zombie accumulation that led to the prior
357-file cleanup. Deletion is header-guarded, so any hand-edited file
that loses the auto-generated marker is preserved and reported.

This is the first-adoption baseline; prune activates on the next regen.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: gjtorikian