fix: address CI lint errors (gosec, errcheck, unparam, duplicate tests) (#730)

* fix: address CI lint errors (gosec, errcheck, unparam, duplicate tests)

- Remove duplicate TestHandleDelete_DryRun and TestHandleDelete_PartialSuccess
  from server_mutations_test.go (already defined in server_delete_test.go)
- Add nolint:gosec comments for exec.CommandContext calls in sync_branch.go
  (variables come from trusted config/git sources)
- Fix gosec G304/G306 in yaml_config.go (file read/write permissions)
- Fix errcheck in mol_run.go (templateStore.Close)
- Add nolint:unparam for updateYamlKey error return

* fix: add remaining nolint:gosec comments for exec.CommandContext calls

- sync_branch.go: diffCmd, logCmd (dry-run), commitCmd, pushCmd, remoteCmd
- sync_check.go: checkLocalCmd

* fix: add more nolint:gosec comments for exec.CommandContext calls

- sync_branch.go: pullCmd
- sync_check.go: localRefCmd, remoteRefCmd, aheadCmd
- sync_import.go: checkoutCmd

* fix: add final nolint:gosec comments for exec.CommandContext calls

- sync_check.go: behindCmd
- sync_import.go: fetchCmd

---------

Co-authored-by: Charles P. Cross <cpdata@users.noreply.github.com>

cmd/bd/mol_run.go

@@ -94,7 +94,7 @@ func runMolRun(cmd *cobra.Command, args []string) {
 			fmt.Fprintf(os.Stderr, "Error opening template database %s: %v\n", templateDB, err)
 			os.Exit(1)
 		}
-		defer templateStore.Close()
+		defer func() { _ = templateStore.Close() }()
 	}
 
 	// Resolve molecule ID from template store