allow the user to tune clustering parameters and make sure transformations are sorted before trimmed

git-svn-id: https://svn.salilab.org/imp/trunk@16221 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add refinement stage

git-svn-id: https://svn.salilab.org/imp/trunk@16222 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing #include lines

git-svn-id: https://svn.salilab.org/imp/trunk@16223 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing #include

git-svn-id: https://svn.salilab.org/imp/trunk@16224 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing #include

git-svn-id: https://svn.salilab.org/imp/trunk@16225 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing include

git-svn-id: https://svn.salilab.org/imp/trunk@16226 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove file lists from SConscript

git-svn-id: https://svn.salilab.org/imp/trunk@16227 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
replace UNARY_FUNCTION macro

git-svn-id: https://svn.salilab.org/imp/trunk@16228 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
update doc

git-svn-id: https://svn.salilab.org/imp/trunk@16229 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Move the module metadata into a description file that is external to the SConscript to make it more easily accessible

git-svn-id: https://svn.salilab.org/imp/trunk@16230 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
also move applications to description files

git-svn-id: https://svn.salilab.org/imp/trunk@16231 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix example dep build

git-svn-id: https://svn.salilab.org/imp/trunk@16232 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Make the git hook compain when to try to commit things with untracked files lying around. Annoying at first, but quite nice after a bit.

git-svn-id: https://svn.salilab.org/imp/trunk@16233 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove left over tree

git-svn-id: https://svn.salilab.org/imp/trunk@16234 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Pull creation of .i files out into a setup script.

For the first time ever, swig won't rebuild the swig wrappers simply because it computed the dependencies wrong.

git-svn-id: https://svn.salilab.org/imp/trunk@16235 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix fox linking by restoring deleted lines

git-svn-id: https://svn.salilab.org/imp/trunk@16236 e91f8c7b-0e32-4433-a9ac-4502d39a4eab