Patch Set 1: Do not submit

(5 inline comments)

I have to put this down for now, but I'm posting this with notes inline on certain lines of code to at least save my current state and make it visible to everyone else.

I'm rather disappointed in the current performance of PatienceDiff.  It may be because of the sorting of the index; using a hashtable with near constant time insertion might be more efficient.

We may also be looking at a very bad input.  CharArray has skewed semantics where equals() is faster than most other operations.  This isn't true on RawText, or probably any other more complex sequence object.  Trying to avoid equals() only costs us running time, but it should save a lot of time on a more realistic source code-like file.