Update file.py

Moving the changes rejected from 1699 into 1714
Update test_audit_file.py

moving rejected changes from 1699 to 1714
Update file.py

Moving rejected changes from 1699 to 1714
Merge remote-tracking branch 'origin/master' into 1714-file-object-round3
Fixing the audits, adding the upgrades, fixing the inserts
Fixing test_file_upgrade3 to acutally upgrade to 4
Laurence made a fix so that upgrade_tests did not require modern schemas
Merge remote-tracking branch 'origin/master' into 1714-file-object-round3
Really we want to upgrade from 3 not from 2
Fixing upgrade
Audits need the testapp
Making small changes to try to fix the upgrade
The paired_with upgrade will be moved to asynchronous.
No really this should be the kent lab
Merge pull request #386 from ENCODE-DCC/1714-file-object-round3

1714 file object round3