Paths rework

The "run" directory in JTR-jumbo is a mess, so I tidied it up a bit.

The first commit simply moves around some files already present in run/, while the others fixes the paths in the Makefile.

The dfb3c5f771a5a8f744d2484b4d38c6023b25e2b4 commit fixes the path of john.exe in symlink.c.

I've been able to test only the linux-x86-64 build (and everything worked fine there).

The charsets have been moved to $JOHN/run/charsets and their paths have been modified accordingly in john.conf

The dumb32.conf, dumb16.conf and dynamic.conf config files have been moved to $JOHN/run/configs and their paths have been modified accordingly in john.conf

Everything in charge of converting a fileformat to a john-compatible format has been moved to $JOHN/run/xyz2john

The others misc utils and scripts have been moved to $JOHN/run/utils