dagman_multi_dag.cpp/dagman_multi_dag.h: these files are for functions used by both condor_submit_dag and condor_dagman itself. (There are limitations on what can be done in this module so that the link works for both. For example, you can't call debug_printf() because that's only linked in condor_dagman()).
Bootstrapping -- see Dag::Bootstrap() -- need to explain that.