I don't think it should stage untracked files.  Maybe useful for the first day of the project where all files are new, but not helpful later and for folks who have untracked files in their worktree, for whatever reason.  This could be a `cola.syncuntracked` configuration option, which can default to `false`.  See `cola.displayuntracked` and the commits that introduced it for an example of how to add it to the preferences dialog.