Inclusion patterns do not work with multiple `srcDir`s

Example:
```
sourceSets {
main {
proto {
srcDir("directory-1").setIncludes(
listOf(
"file-in-directory-1",
)
)
srcDir("directory-2")
}
}
}
```

In this example, none of the files from the `directory-2` are processed, because the generated `protoc` command applies inclusion filter `file-in-directory-1` to both folders.

Current workaround for this is to explicitly add all files from `directory-2` to `setIncludes` of `directory-1` which can be quite cumbersome.

Reproduce the issue with the provided sourceSets configuration and inspect the generated protoc command. Trace how inclusion patterns are applied across multiple srcDir entries; done means files in directory-2 are processed without requiring them in directory-1's setIncludes.

Written by the indexing model from the issue text.