fix(store): use PASSIVE checkpoint to avoid file-shrink under concurrent readers

cbm_store_checkpoint() invoked SQLITE_CHECKPOINT_TRUNCATE, the most
aggressive mode. When two cbm-mcp processes share a cache dir, one
process's TRUNCATE can shrink files while another has them mmap'd,
raising SIGBUS on macOS. PASSIVE never blocks readers and never
ftruncate()s either file; SQLite still autocheckpoints in PASSIVE
mode at 1000-page boundaries, so reclamation is unaffected for
single-process users.

Recommended by SQLite docs for shared databases:
https://www.sqlite.org/pragma.html#pragma_wal_checkpoint