Add more detail on the EMageFit protocol.


git-svn-id: https://svn.salilab.org/imp/trunk@17234 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Document EMageFit scripts and other tools.


git-svn-id: https://svn.salilab.org/imp/trunk@17235 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Remove PDF manual; up to date and tested information is now present in the
doxygen manual.


git-svn-id: https://svn.salilab.org/imp/trunk@17236 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
use boost.endian instead of our own endian test to close issue #220

git-svn-id: https://svn.salilab.org/imp/trunk@17237 e91f8c7b-0e32-4433-a9ac-4502d39a4eab