Fixes for make dist.

Hadn't done make dist for awhile and it got stale. Main thing here is to note that for templated classes that I've either needed to extend or anticipate user extension, we do two things: 1. We only build an "something_instantiate.C" file that #include file.C (I've opted for this over putting everything in the header in these complex classes). This prevents compiling the same file multiple times, but we have to be sure to... 2. Install and EXTRA_DIST the appropriate file.C files needed to extend the templated classes.

Note that make distcheck isn't working for me, but manually testing works. Opening a different issue for that.