Handle proto.include_dirs for java

The proto_library(s) created for include_dirs will be added to
transitive_deps

This also fixes an existing bug for java_library containing .protos in
srcs via filegroups.
```
java_library {
  name: "foo",
  srcs: ["foo.proto", "foo_filegroup"],
}
```

At ToT, foo_filegroup was missing from the equivalent proto_library in
bp2build workspace.

Bug: 285140726
Test: allowlisted pandora-proto-java and built that
Change-Id: I2657d8cdef2e47434bc3e0d09a074c8e27299afc