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feat: merge pristine.redb and changes.redb into atomic.redb - #230
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Repositories kept graph state in .atomic/pristine.redb and the provenance journal in .atomic/changes.redb. Both now live in one .atomic/atomic.redb. - atomic-core: a registry of every table (pristine/schema.rs) with a schema version in the new atomic_meta table. LegacyDatabases::merge_into copies each table through its typed definition into a fresh file, verifies a per-table digest against the source, refuses unknown non-empty tables, and leaves retired tables (stacks, channels, file_mtimes) behind. - atomic-repository: ensure_database merges a legacy layout on first open (atomic.redb.merging -> atomic.redb; old files kept in .atomic/legacy/<ts>/) and finishes an interrupted retirement. Concurrent openers serialize on the legacy file lock. open/open_existing/open_readonly wait up to 5s for a busy database. The change store can share the repository's redb handle (Repository::redb_change_store) or open an existing file without creating it. - atomic agent database-owner: opens atomic.redb only while serving a store request. Startup, Ping and Shutdown never touch it, so the owner no longer locks other atomic processes out of the repository. - hooks: close the repository before acknowledging a checkpoint, since the owner now opens the same file.
vinceblock99
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October 2, 2026 02:50
geekgonecrazy
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- state.change_store: ensure_database (the legacy-layout merge) then open_existing on the merged atomic.redb — redb refuses a second concurrent handle, so the journal-port handlers keep the sequential open/use/drop discipline under the gate. - DirectJournalSink holds NO handle: each journal operation opens the merged database, runs, and drops it (the orchestrator opens the same file; the two can no longer coexist as concurrent handles). - atomic-repository: sync the #230 database module (pub database mod for the CLI's root-finder predicate) + the CandidateSet/BaggageEntry/ Coverage Deserialize derives for the triage wire.
geekgonecrazy
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Oct 7, 2026
#230 merged pristine.redb and changes.redb into a single atomic.redb, so a fresh init no longer writes pristine.redb — but the CLI's root finder still required it and could not discover #230-created repos at all. The finder now applies the same predicate Repository::find_root uses (has_database: atomic.redb, or the legacy pristine.redb before the merge), and the discovery integration test asserts the merged database file.
geekgonecrazy
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Oct 7, 2026
- state.change_store: ensure_database (the legacy-layout merge) then open_existing on the merged atomic.redb — redb refuses a second concurrent handle, so the journal-port handlers keep the sequential open/use/drop discipline under the gate. - DirectJournalSink holds NO handle: each journal operation opens the merged database, runs, and drops it (the orchestrator opens the same file; the two can no longer coexist as concurrent handles). - atomic-repository: sync the #230 database module (pub database mod for the CLI's root-finder predicate) + the CandidateSet/BaggageEntry/ Coverage Deserialize derives for the triage wire.
geekgonecrazy
added a commit
that referenced
this pull request
Oct 7, 2026
#230 merged pristine.redb and changes.redb into a single atomic.redb, so a fresh init no longer writes pristine.redb — but the CLI's root finder still required it and could not discover #230-created repos at all. The finder now applies the same predicate Repository::find_root uses (has_database: atomic.redb, or the legacy pristine.redb before the merge), and the discovery integration test asserts the merged database file.
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Merge
pristine.redbandchanges.redbinto.atomic/atomic.redbso repository state uses one database file.This PR covers database consolidation. Cross-table publication transactions and additional agent crash recovery are separate follow-up work. Protobuf/RPC contracts are unchanged.
Validated with the full workspace suite (9,116 passed), agent harness, real legacy repository migration and live Codex hook workflow; Clippy, rustdoc and formatting checks pass.
Before release, coordinate the matching
atomic-storageupdate for its directpristine.redbaccess and snapshot names.