How can I modify scripts inside of a registry package?
(I’m not talking about the usual downloade assets from the Asset store but registries that are added in the manifest.json file of the project)
If they’re downloaded from a registry, they’re assumed to be immutable. If you change them, those changes will be discarded.
You can find the files and copy the package to your packages folder to have a local copy instead, but then they’re not registry packages anymore, if that’s a problem.
I’m pretty sure the packages gets copied to your Library’s packagecache, so that’s where you’d copy it from.
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Thanks 
Another question: how can I reference a class of my other scripts in the package scripts?
You can’t reference your general code from packages, the dependency is the other way around.
If this is general purpose code, you can extract it into a package and reference it from your package, but if that’s a good idea or not very much depends on your project!
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