Move the "Fixes" file into the commit log where it belongs

Commit e518fa86073f3f57e57775baf42911b3cbfb0f4f
Transitions now conditioned on hidden state length.
Also, Aligner calls method in original align.py to fetch emission
paramaters trained by IBM Models.
Trained IBM Model 1 on 10000 sentence pairs for 10 iterations followed
by 3 iterations of HMM on 10000 sentences pairs.
AER of .45 was  obtained.

Commit 2b6a8070239532ca8e0300a69694a68904310757:
Refactored Likelihood computer into a class. Also, bypassed parameter
initializer.
Initialization is now done "on the fly" during Likelihood computation.
Speedup of about 1 minute .
Currently takes 3 minutes for 1000 sentence pairs for 5 training
iterations.

Commit 941e36656fea5c15e274ed461debfe15dcac5654:
Added The decoder module. Need to test for bugs.

Commit 51ecce97be0b490ab315997dcfd3021ed746a881:
Re-factored into classes.
Fixed training to go over all training instances.
Fixed a serious underflow issue that was causing division by zero errors
all over the place.

Resulting algorithm seems to be working fine except I'm not sure that it
is fast enough.
I created a small test set of 20 sentences to test and it still takes a
few seconds to compute indicating that doing training over the entire
set may be prohibitive as of now.