Update referenceStructure.avdl

Merging together referenceStructure.avdl and referenceAlignments.avdl
Delete referenceAlignments.avdl

Moved contexts to referenceStructure.avdl
Update referenceStructure.avdl
Merge pull request #50 from benedictpaten/master

Merging referenceAlignments.avdl into referenceStructure.avdl