chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)

- Remove TestFindJSONLPathDefault from .test-skip (now passes)
- Add explanatory comments to 24 ignored error locations in cmd/bd:
  - Cobra flag methods (MarkHidden, MarkRequired, MarkDeprecated)
  - Best-effort cleanup/close operations
  - Process signaling operations

Part of code health review epic bd-tggf.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/mol_spawn.go

@@ -256,7 +256,7 @@ func init() {
 	molSpawnCmd.Flags().String("attach-type", types.BondTypeSequential, "Bond type for attachments: sequential, parallel, or conditional")
 	molSpawnCmd.Flags().Bool("pour", false, "Create persistent mol in .beads/ (default: wisp in .beads-wisp/)")
 	molSpawnCmd.Flags().Bool("persistent", false, "Deprecated: use --pour instead")
-	_ = molSpawnCmd.Flags().MarkDeprecated("persistent", "use --pour instead")
+	_ = molSpawnCmd.Flags().MarkDeprecated("persistent", "use --pour instead") // Only fails if flag missing
 
 	molCmd.AddCommand(molSpawnCmd)
 }