SetReadyBit: non-atomic read-modify-write of PRAGMA user_version

[Widthdom]

Summary

SetReadyBit() reads PRAGMA user_version, OR-s a flag, then writes back via separate statements with no atomic wrapper. Two parallel cdidx runs (e.g. CI + a local rebuild) can each read 0, then write 0|FlagA and 0|FlagB; whichever runs second overwrites the other's flag.

Evidence

• src/CodeIndex/Database/DbWriter.cs:2028-2035 — SetReadyBit reads then writes user_version in two separate statements.

Impact

• fold_ready / graph_table_available / issues_table_available may report false even after both runs completed successfully.
• Status / readiness output silently misleads the user about what trust paths are available.

Proposed direction

• Wrap the read-modify-write in a single transaction (BEGIN IMMEDIATE … COMMIT).
• Or: switch to a separate metadata table with a row-level UPSERT for each flag, since user_version was never designed as a bitset.

Repro env

• Branch: main @ 2ee912d (release v1.21.0)

[Widthdom]

Work started on branch fix-issue1513.