fix: make SQL mutations atomic and durable

[j6k4m8]

Summary

• commit public SQL mutation methods automatically
• roll back failed mutations instead of leaving partial state
• keep multi-step node and edge changes in one transaction
• isolate duplicate-edge insert failures with a savepoint before metadata updates
• preserve explicit commit calls for compatibility
• cover reopen persistence, edge updates, removals, and rollback behavior

[codspeed-hq]

Merging this PR will not alter performance

✅ 8 untouched benchmarks

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_{Comparing fix/sql-transactions-70 (309996d) with master (a2b963f)}