Doxygen Fixes, master branch (2019.01.21.)

This is to address ATLINFR-2883.

In order to make doxygen and dot functional with LCG_94, I had to do two things:

• Make sure that FindDoxygen.cmake would recursively set up all packages that it needs for its runtime environment;
• Update the AtlasCMake code to execute the doxygen command through atlas_build_run.sh to make sure the executable sees the "correct" environment.

With these updates I was able to produce reasonable looking pages on top of the master branch of atlas/athena.