ensure "make distcheck" works

This commit ensures "make distcheck" works, which is critical for making
sure release packages will build and install properly. Add generated
protobuf files and generated release tarballs to .gitignore. Remove
compiler include directives for src/include and src/internal and use those
directory prefixes directly in the source #include directives. Add
generated protobuf files, src/include, and src/internal to distribution.