Added cell overlap checking subroutine
Made plots check for cell overlaps by default
Added command-line flag to enable cell overlap checking during transport
Added output summary for cell overlap checking
Added support for parallel runs to geometry overlap checking
Updated documentation with overlap checking
Restructured how MPI and HDF5 are treated in Makefile.
Remove -DNO_F2008 for gfortran.
Changed F90 to FC in Makefiles.
Revert "Changed F90 to FC in Makefiles." FC was overwritten if PETSC=yes because of an include file.

This reverts commit 1a6f7a1b9aa935ad7841713a5b5551f0e548f834.
Added -g to print_usage.
Merge branch 'cell_overlap_check'

Conflicts:
	src/initialize.F90
Combine -r and -s options in man page.
Made numerous Python scripts in utils work with either 2 or 3.
Write warnings to stderr instead of stdout.
Fix test_particle_restart.
Add release notes for 0.5.2 and increment version numbers.
Update DEPENDENCIES.