Lttoolbox provides a module for reordering separable/discontiguous multiwords and processing them in the pipeline. Multiwords are manually written in an additional xml-format dictionary.
Prerequisites and compilation are the same as lttoolbox and apertium. See Installation.
On Debian/Ubuntu derivatives, it is part of the nightly repo as sudo apt-get install apertium-separable.
The code can be found at https://svn.code.sf.net/p/apertium/svn/branches/apertium-separable and instructions for compiling the module are:
svn co https://svn.code.sf.net/p/apertium/svn/branches/apertium-separable
./autogen.sh
./configure
make
make install