Update and rename referenceHierarchy.avdl to referenceAlignments.avdl

Sorry to hijack this file, I'm proposing to generalise it to represent alignments, with two possible constructs - the alignment block and a cigar alignment. The alignment block is a pairwise structure that matches intervals between two blocks, and can be placed in an array to describe a pairwise alignment. The second alignment structure is a CIGAR based alignment that apes the basic CIGAR format, with the difference that the alignment is between to paths in two sequence graphs.
Update referenceAlignments.avdl

Fixing typos.
Update referenceAlignments.avdl

Simplifying to just represent cigars
Update referenceAlignments.avdl

Adding in alignment from sequence to sequence graph.
Updating everything to compile.

Also Proposing some changes to schema naming, and adding a stub ga4gh.avdl.

What we really need to do is have one repo for all the GA4GH schemas that's flat and includes *just* the .avdl files, so they can be included as a submodule. That or invent much more sophisticated Avro dependency management.