gnupg-for-java: remove unneeded autogenerated JNI headers

I think this are only used for C++, but right now they are just another
file to maintain while providing no benefit to us.  They can be updated in
the gnupg-for-java project once development settles down.
gnupg-for-java: add GnuPGKey.hasSecretKey() to report if any subkey is secret
fix compile warnings in pinentry_cmd_handler.c
gnupg-for-java: fix compiler warnings