Solutions to known issues

[pgavigan]

I recall from discussing with Sacha that there is a know issue related to a few jLOAF dependencies needing manual configuration. This process needs to be documented. I know I was able to solve it last week but I can't remember how this week. :(

I'm referring to the matlabcontrol, sqlite, and commons-math.

[sachag678]

looking into it atm.

[sachag678]

https://help.github.com/articles/removing-files-from-a-repository-s-history/