feat(ci): real-time quality gate streaming, re-entrant rate limit locking, and repos clone destination

[dan-petty]

Deliverables & Scope

1. Real-time CI Streaming: Stream live check badges and duration as concurrent checks complete; surface running status for long-running tests.
2. Re-entrant Rate Limiter File Locking: Implement thread-local lock depth tracking in _disk_quota_lock to eliminate self-deadlocks during nested rate limit calls; enforce mandatory uniform pacing.
3. GitHub Projects Quota Safety: Guard against GraphQL quota depletion using _is_graphql_quota_exhausted and cap mutations per sync run.
4. Dynamic Repo Clone Destination: Parse organization/owner from Git clone URLs (repos//) rather than hardcoding _standalone.