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refactor(persistence): unify SQLite to single deerflow.db and move checkpointer to runtime
Merge checkpoints.db and app.db into a single deerflow.db file (WAL mode handles concurrent access safely). Move checkpointer module from agents/checkpointer to runtime/checkpointer to better reflect its role as a runtime infrastructure concern. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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@@ -740,8 +740,8 @@ skill_evolution:
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# backend: sqlite -- Single-node deployment, files in sqlite_dir
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# backend: postgres -- Production multi-node deployment
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#
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# SQLite mode automatically uses separate .db files for checkpointer
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# and application data to avoid write-lock contention.
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# SQLite mode uses a single deerflow.db file with WAL journal mode
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# for both checkpointer and application data.
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#
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# Postgres mode: put your connection URL in .env as DATABASE_URL,
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# then reference it here with $DATABASE_URL.
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