Incremental build is broken for external packages with patches

[ViktorHofer]

https://github.com/dotnet/source-build-reference-packages/blob/a2143ed684ba97f3cf65964fdef8d5fae0ebcda6/src/externalPackages/projects/Directory.Build.targets#L15-L47

1. The PrepareInnerClone target always runs but skips unchanged files.
2. The ApplyPatches target which runs after PrepareInnerClone only runs once successfully as it then creates an output marker file.

If something fails in the SBRP repo and I run the build again, the PrepareInnerClone target runs again and overwrites the patched files but the ApplyPatches target doesn't run anymore.

[MichaelSimons]

This appears to be the same issue described in #1310.

[ViktorHofer]

I would probably just remove the Inputs & Outputs from the target that applies the patches. That means that incremental builds are not really incremental for SBRP components but better than the current situation. We need to always copy files as otherwise the "clone" directory from which we build the submodule doesn't receive code edits.