The atom::BondPairContainer has been renamed to atom::BondPairFilter since it wasn't a real container. A real atom::BondPairContainer has been added.
Out of source builds mostly works. To do an out of source build, make a link to scons_tools and SConstruct from the source directory in the build directory and then add the line
repository="../path_to_src_dir"
in the config.py in the build directory. Then running scons in the build directory will put generated files there. This allows you to make both a release andfast build off of the same set of sources. Proper docs will be added soon.
The SConscript setup for a module has been greatly simplified so it should be easy enough for users to maintain their own module and updates to the build system shouldn't involve changes to user SConscripts any more. This does mean that any non-svn modules need to be updated. Look at IMP.core or another module and copy what is there. Again, proper docs will be added soon.