Massively rework eland file finding and indexing.

Massively rework eland file finding and indexing.
Instead of looking in known locations for specific file names
in priority order, this now scans the gerald tree looking for
any potential eland files.

The eland container class has been changed to be a MutableMapping and
the found files are added. The class internally tracks the priority of
the different file types and will drop any lower files when a higher
priority file shows up.

In addition the key for finding files is now a "SampleKey" class
which supports tracking sample name, lane and read. The SampleKey
also has a fuzzy matching feature that uses "None" as a wildcard.

So you can search for all the samples for a particular end with
something like "SampleKey(read=1)". Needless to say this change
required updating a lot of code that was assuming the nested
list/dictionary structure from before that was tracking read/lane.