Add --save flag to persist defaults into the manifest

`--save` should be conservative: add new actions, leave the existing ones in the manifest intact. We might want a `prune` command to remove manually deleted actions.

Start by locating the CLI entry point for `--save` and the code that updates the manifest. Check how actions are read and written, then verify that saving adds new actions while preserving existing manifest actions. The issue mentions a possible `prune` command, but does not define it as part of this change.

Written by the indexing model from the issue text.