There'll be some that don't need to use manifest_version 2, and can be easily downgraded...
Some might not be so easy
Simple modifications (removing value):
- GeoData
- GlobalBlocking
- JsonConfig
- LiquidThreads
- OAuth
- PagedTiffHandler
- PageForms https://gerrit.wikimedia.org/r/#/c/319499/
- PageImages
- ThrottleOverride
- ZeroPortal
More extensive modifications (moving things to onRegistration):
- BlockAndNuke
- timeline
- TorBlock
- TrustedXff
- ZeroBanner