A couple of bugs in the boost wrapper and python interface that caused initializing a simulation from a binary file to fail/

refs #2482
Note that binary dump format is deprecated

Updated the documentation for init.read_bin and dump.bin to note that
they are deprecated. Also added a list of unsupported features.

refs #2482
Merge read-bin-fixes: fixes #2482

* read-bin-fixes:
  Note that binary dump format is deprecated
  A couple of bugs in the boost wrapper and python interface that caused initializing a simulation from a binary file to fail/