Add brkfix to goma, feedback needed

Looking for feedback on brkfix integration

Here is a better diff of what was modified in goma https://gist.github.com/wortiz/3f673e874a3f6f1fa80f

Documentation describing the interface can be found here: https://github.com/wortiz/goma/blob/brkfix-fb/docs/parallel_integration.md

I added a new file called `brk_utils.c`

I also added `brk_exo_file.c` and `fix_exo_file.c` under brkfix which are mostly copies of brk.c and fix.c but with an easier to use function interface for goma.

I haven't broken any backwards functionality as far as I know, my input file additions are optional and goma will still run in the same fashion if run without the new options

Basic usage:

```
goma -a -i input -brk brkfile
```

or specify brkfile in input file with `Brk file`

goma must be run in serial to create a brkfile and will exit if run on parallel with -brk or `Brk file` specified.

If the brkfile exists then goma can be run in parallel

```
mpirun -np 4 goma -a -i input -brk brkfile
```

`-brk brkfile` again can be specified in the input file, and goma will "fix" the output exodus file based on the `Fix Frequency` card, if the fix frequency isn't specified goma will only fix the output at the end of main.c after the problem has been "solved"

I still need to add a -fix flag which will fix the broken exodus files manually (similar to fix executable)


Having this Brk_Flag be a global variable is a very poor code practice.  I'm not sure if this is something you copied from elsewhere or not, but I'd prefer you not use this long term.  It's much better to have some object that owns it, or at least have it be a member variable on some struct.  

I'll go ahead and pull with this in there, but please make a plan to move this to a better scope.