Compose ReferenceSet.md5 from all Reference.md5

This was originally proposed on ga4gh#66 by @vadimzalunin. The advantage of this approach is that computation of ReferenceSet.md5checksum is strictly easier than the original definition. Furthermore, it should have indistinguishable uniqueness guarantees.

Examples of implementation difficulties with the original approach:
- To create a new ReferenceSet, I need to fetch all sequence data contained within all references. The md5s are more likely to be readily available e.g. in the SAM header.
- To create a new ReferenceSet and corresponding References, I would need to compute md5 sums over all sequence data twice.
- To create a new ReferenceSet which uses existing References, but differs only in order from an existing ReferenceSet, I would need to compute and md5 over all Reference.sequence again.

Also makes Reference.name non-nullable, as the semantics of performing an md5 over a null reference name are/were not defined.
Merge branch 'master' of https://github.com/ga4gh/schemas

Conflicts:
	src/main/resources/avro/reads.avdl
Drop ReferenceSetId from SearchReads

This can be inferred from the context of the search, e.g. I search a given set of ReadGroups which are aligned to ReferenceSets, I shouldn't need to specify the ReferenceSet twice.
Merge branch 'master' of https://github.com/ga4gh/schemas into patch-4

Conflicts:
	src/main/resources/avro/readmethods.avdl
Merge pull request #115 from calbach/patch-3

Compose ReferenceSet.md5 from all Reference.md5
Define GET /reference/{id}/bases in favor of GAReference.sequence.
Update various Reference{,Set} semantics.
Add pageSize field to all search methods
Improve consistency for reference methods

- `md5checksums` is consistent with `GAReference::md5checksum`.
- Support repeated md5/accession filtering in SearchReferenceSets, to be consistent with SearchReferences.
Merge pull request #129 from calbach/patch-5

Improve consistency for reference methods
Merge pull request #120 from calbach/ref-bases-rds

Define GET /reference/{id}/bases in favor of GAReference.sequence.
Constrain the outgoing reference bases alphabet
Add variant sets search method
Merge pull request #133 from calbach/patch-6

Constrain the outgoing reference bases alphabet
Merge pull request #128 from calbach/many-refs

Update various Reference{,Set} semantics.
Merge pull request #123 from cassiedoll/maxresults

Add pageSize field to all search methods
Merge pull request #117 from calbach/patch-4

Drop ReferenceSetId from SearchReads
First version of metadata
make all IDs global
Update line indents to match style in #111