onboard: add step to commit JSONL with code changes (#154)

Add a new step to the onboarding workflow reminding AI agents to commit
the `.beads/issues.jsonl` file together with code changes. This ensures
issue state stays synchronized with code state, which is critical for
maintaining accurate project history and making issues meaningful when
reviewing past commits.

cmd/bd/onboard.go

@@ -66,6 +66,7 @@ bd close bd-42 --reason "Completed" --json
 4. **Discover new work?** Create linked issue:
    - ` + "`bd create \"Found bug\" -p 1 --deps discovered-from:<parent-id>`" + `
 5. **Complete**: ` + "`bd close <id> --reason \"Done\"`" + `
+6. **Commit together**: Always commit the `.beads/issues.jsonl` file together with the code changes so issue state stays in sync with code state
 
 ### Auto-Sync