Revert "Added some src/ stuff to make distribution hopefully work"

This reverts commit 4e9038038fc3ee62863762e07f17fb0f64908305.
using recursive make in the src/ directory
compile and link executables inside of src/
removing automatically generated files
creating recursive make rules for the documentation
ignore more output files
do not make cpp files executable
adding `doc' target
need to ship softpars.cpp and softsusy.cpp
need to ship *.tex files as well
define docdir for Automake < 1.10
added to the acknowledgements.
Merge branch 'nmssm2' of https://github.com/Expander/softsusy into nmssm2
Merge branch 'recursive-make' of https://github.com/Expander/softsusy
Merged files in from recursive branch
Removed errant TODO items that are addressed