Replace with markdown explicit links.


git-svn-id: https://svn.salilab.org/imp/trunk@17476 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Add back mysteriously disappeared links; use markdown syntax; fix links to
application overview pages.


git-svn-id: https://svn.salilab.org/imp/trunk@17477 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Replace with a much smaller system, to speed up the test.


git-svn-id: https://svn.salilab.org/imp/trunk@17478 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
If no good scoring solution is returned, report an identity (not garbage)
transformation. Closes issue #214.


git-svn-id: https://svn.salilab.org/imp/trunk@17479 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
minor readme cleanups

git-svn-id: https://svn.salilab.org/imp/trunk@17480 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
rewrite setup_git in python

and add support for running it in a module not in the main IMP repository

git-svn-id: https://svn.salilab.org/imp/trunk@17481 e91f8c7b-0e32-4433-a9ac-4502d39a4eab