Merge pull request #32 from raymond301/master

Fixed Graph/Meta bug
Fixing Sequest tests. Trying to determine what keeps Sequest from closing files.
Concat file starts/ends transactions.
Cleaning up QuaMeter check.
Fixing the migration script.
Cleaning up the remains of the migration script.
Quameter renames instruments on the server.
Mistake - specific to atlas_migration schema.
Work in progress - QuaMeter loads protein counts into the database.
Documentation cleanup
Renaming curation dao to be consistent with other classes.
Specifically naming the index.
Forgotten TestDataProvider interface.
Starting to test the database layer.
In order to test QuaMeter, we need to have some data in place so it even works.
Testing of QuameterDao in progress  - it requires a fully populated database to ensure all is well.
'file' is a reserved keyword in MS SQL Server.
Adding test install for dao objects.
 - unimod is faster for tests, loads just two mods
 - log4j is automatically enabled
 - FileSearch has bidirectional relationship with SwiftSearchDefinition
 - slf4j facade fixed
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Fixing the inter package loop.
added custom colors ability to unhide previously hidden data points.
minor js update