Update manifest.py to allow overlays of init functions

[runcows]

Cherry picking from #1168

Small update to the manifest plugin to allow overlays of init.
While currently we do not have any overlays of init functions, the current behaviour is undocumented and confusing.
I've had issues with this behavior before (resolved in #1099 commit [ec0e9fc])

[SpecialBuilder32]

So what's the use-case for needing overlays of init? I would argue from a design standpoint init should be constant throughout any overlayed versions, especially since its main purpose is to start clocks and define scoreboards and other constants. I worry that multiple copies of init could cause confusion where it's not really needed.

[runcows]

I can't argue with that, and can't provide any use-cases right now.
However, there has already been one instance where an overlay of init has made it past review, in Blossoming Pots first PR (#1070). Not supporting overlays of init feels like begging for more similar issues, since things like this can and will be missed in review.
If for no other reason than to save ourselves that trouble later, I think we should support overlays of init, even if we don't endorse them.

[SpecialBuilder32]

...so I'm not sure why this was merged.

Anyway @runcows, so what did you use an init overlay in Blossoming Pots then? I'd consider that a use-case, but I can't tell from just looking at the code itself.

[runcows]

Yeah, I had, but the reason for it was silly. I was using it to check the version of the big data storage to see if it needed to be changed. Overlaying init was to check if the current overlays format was loaded. It was a holdover from how I had blossoming pots before GM4 and definitely not necessary. That, in combination with the overlay of init breaking versioning through manifest, is why I removed the overlay in #1099.