Adding logging for IOExceptions in FileSerializer

Fixes https://www.pivotaltracker.com/story/show/58845340
Merge pull request #12 from futures/file-permissions-bugfix

Adding logging for IOExceptions in FileSerializer
Resolves: https://www.pivotaltracker.com/story/show/58845340
Fixing queries used in waitForTriples calls to be the same as other checks (fixes http://www.pivotaltracker.com/story/show/61351914)
Merge pull request #13 from futures/test-query-bugfix

Fixing queries used in waitForTriples calls to be the same as other checks

Addresses: https://www.pivotaltracker.com/story/show/61351914 (on Mac OSX, not on Linux)