3ds: Makefile improvements
- Allow overriding of the smdhtool and 3dsxtool programs
- Introduce dependencies in ctru.make for 3dsx and cia packages
- Build these packages when the binary is built
- Copy instead of moving the cia package when building a zip
- Properly clean all build artifacts when make clean is used
Change-Id: I2069bcc44d6ab6031ef61ed9980f92ff9a913bc9