Limit manifest modifications to in-memory

[noahnu]

Is your feature request related to a problem? Please describe.

No need to backup and restore package.jsons as we can make modifications in memory prior to publish without having to write to disk.

Describe the solution you'd like

Remove the export manifest logic when "patching". We may then want to change the persist versions logic to a distinct step and support only modifying the version and not dependencies when persisting. (Would still need to modify dependencies for publish though, but it causes issues if committing it to git)

Describe alternatives you've considered

Additional context