The JSONL file hash mismatch warning was appearing consistently after
git commit operations, even when no actual data inconsistency existed.
Root Cause:
Two code paths export to JSONL but only one updated jsonl_file_hash:
- flushToJSONLWithState() (used by bd update/create): Updated both
jsonl_content_hash AND jsonl_file_hash
- finalizeExport() (used by bd sync --flush-only): Updated only
jsonl_content_hash, NOT jsonl_file_hash
Since validateJSONLIntegrity() checks jsonl_file_hash, any bd command
after a git commit would see a mismatch and trigger the warning.
Steps to Reproduce (before fix):
1. cd /path/to/beads-project
2. bd update -p 3 some-issue-id # Works fine, stores hash H1
3. git add .beads/issues.jsonl && git commit --amend --no-edit
# Pre-commit hook runs bd sync --flush-only
# This updates jsonl_content_hash to H2 but leaves jsonl_file_hash as H1
4. bd update -p 3 some-issue-id # WARNING appears!
# validateJSONLIntegrity() compares file (H2) with jsonl_file_hash (H1)
5. Repeat steps 3-4 indefinitely - warning always appears
The fix adds SetJSONLFileHash() call to finalizeExport(), ensuring both
export paths update the same metadata consistently.
493b7008a2