Fix a few more problems with automake 1.14 and the changes made for it.

1. The dis_read.c file wasn't copied over to the mom and needed to be.
2. CXXFLAGS never got set with -g if --with-debug was configured,
  meaning debug symbols didn't load.
3. There were two FUNCTION_TIMER statements in node_manager.c, making it
so that the server didn't compile with CAN_TIME defined.