Remove FS_CGAME_REF and FS_ClearPakReferences

FS_CGAME_REF was used by pure system code that I removed. It was used for sending checksum of pk3 that cgame.qvm is in to server.
Made referenced a qboolean, not storing flags anymore.
All of the FS_ClearPakReferences usages don't make sense.
- FS_Restart called it after freeing all the pk3s, so didn't do anything.
- sv_init.c called it before FS_Restart, which free all the pk3s and then tries to clear referenced flags.
- CL_Vid_Restart_f called it to clear cgame flag, which Spearmint doesn't care about.