Fixed make distcheck. Partial fixes for Bug #769353

Revert changes to Makefile.am, GXml will use its workaround
for build using C files, while Automake Bug #13002 is fixed
for proper Vala support; without it make distcheck will fail
due to trying to write down stamps in a read only directory.

Reverted to changes to install VAPI in Vala versioned directory
thanks a suggestion of Yannick Inizan on Bug #769353. This will
require further tests due to gxml compilation inside flatpak
packages and sanboxed environments.