fix: batch semantic link apply checkpoints

[acidkill]

Summary

• Checkpoint semantic-link synapse application in groups of at most 50 candidates.
• Flush partial groups before budget pauses and retain resumable cursor/counters.
• Add interruption, payload-size, lease-loss, and changed-row regression coverage.

Why

The apply stage rewrote the full pending manifest after each synapse, amplifying checkpoint traffic for large candidate sets. Bounded groups reduce repeated payload writes while preserving the per-candidate budget check and the existing idempotent replay/source-fence protections.

Test plan

• pytest tests/ -m "not stress" against disposable local SurrealDB 3.2.4: 7,867 passed, 50 skipped, 32 deselected, 1 xfailed.
• ruff check src/ tests/ clean.
• ruff format --check src/ tests/ clean.
• mypy src/ --ignore-missing-imports clean.
• Focused semantic-link resume module: 38 passed.
• Disposable database and sanitized environment; no production endpoint used.

Verified by

@acidkill.