Retain dirty runtime failures as partial progress

[yvette-carlisle]

Summary

• Promote dirty retained worktree failures to retained partial progress disposition instead of terminal failure.
• Preserve the source runtime failure class in ledger evidence.
• Add regression coverage for repo-gate, app-server/preflight, stalled reconciliation, and manual-attention guardrails.

Verification

• cargo make fmt-check
• cargo make check-rust
• cargo make test