Modify store, add fetch_all_by_Variation_dbID

Change store to use _variation_id instead of going
through the variation object. Don't need variation
objects unless we are merging.

fetch_all_by_Variation_dbID is a convenience
method useful for doing things like merging split
rows in the table
Merge branch 'master' of github.com:Ensembl/ensembl-variation