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RF: Set BUILDDIR/CUDABUILDDIR so that depend.mk file is correctly generated

Paul McCarthy requested to merge doc/makefile into master
  • Add an example of compiling against a different CUDA toolkit version into the Makefile comments.
  • Set the BUILDDIR and CUDABUILDDIR variables so that they can be used by the depend.mk rule (defined in $FSLDIR/config/rules.mk in the fsl/base> project) to generate correct target names for automatically generated dependencies.
  • We can also remove hand-curated dependencies for .cu object files, as these are now automatically added to depend.mk

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