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)


I was using it as something to get it working without large portions of code change, it doesn't seem like there are any appropriate structures for these kind of flags. So I used a global flag similar to the others in `rf_io.h`

If you have any recommended structures I missed I can take a look at them to avoid the global flag. (Problem_Description seems like the closest but none of the other IO related information was there).

Otherwise there are a lot of these things that should probably be improved on so we can avoid using separate global values.