sync RMF to f58a8dfb1ab2f43d691966717c60851bb68c0e24

git-svn-id: https://svn.salilab.org/imp/trunk@16528 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix printing of ParticleIndexes

git-svn-id: https://svn.salilab.org/imp/trunk@16529 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix bug in (broken) external builds

git-svn-id: https://svn.salilab.org/imp/trunk@16530 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
clean up and test re-reading of restraint particles in rmf files

git-svn-id: https://svn.salilab.org/imp/trunk@16531 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix location of doxygen file.


git-svn-id: https://svn.salilab.org/imp/trunk@16532 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Skip if repository is current directory.


git-svn-id: https://svn.salilab.org/imp/trunk@16533 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
corrected AIC and BIC output. Now using likelihood instead of (incorrect)
posterior


git-svn-id: https://svn.salilab.org/imp/trunk@16534 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
removed rescale*.npy debug output files


git-svn-id: https://svn.salilab.org/imp/trunk@16535 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix spelling.


git-svn-id: https://svn.salilab.org/imp/trunk@16537 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
sync RMF 9ff073472102dccf99526373112c83d9b6151585

git-svn-id: https://svn.salilab.org/imp/trunk@16538 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
regularize compiler config macro defines

git-svn-id: https://svn.salilab.org/imp/trunk@16539 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
simplify config by moving various things out of sconscipts

git-svn-id: https://svn.salilab.org/imp/trunk@16540 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
move spelling list into test

git-svn-id: https://svn.salilab.org/imp/trunk@16541 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
simplify how data is found

git-svn-id: https://svn.salilab.org/imp/trunk@16542 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
move module configure to outside scripts so there really isn't much of anything left in sconscripts

git-svn-id: https://svn.salilab.org/imp/trunk@16543 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove some uses of removed macro

git-svn-id: https://svn.salilab.org/imp/trunk@16544 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
popping up pdfs is kind of annoying, especially now that preview remembers the windows that were open last time

git-svn-id: https://svn.salilab.org/imp/trunk@16545 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
make sure hdf5 stuff is nicely recursively included

git-svn-id: https://svn.salilab.org/imp/trunk@16546 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
lib_only_required_modules aren't supported any more

git-svn-id: https://svn.salilab.org/imp/trunk@16547 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
postpone swig file generation until after configuration as we can do that now

git-svn-id: https://svn.salilab.org/imp/trunk@16549 e91f8c7b-0e32-4433-a9ac-4502d39a4eab