Fix for bug303. The problem was with function applications that get normalized when...

Fix for bug303. The problem was with function applications that get normalized when added to the term database. For example, if x=y exists, and the term f(x) is added, f(y) was stored. So, when getExplanation(f(x), f(y)) was called, trouble ensued. I now keep the original version so that explanations can be properly produced.

Also added theory::assertions debug flag that will printout assertions of each theory for ease and uniformity of debugging in the future.