Fix bug in T index bounds check

See: http://fiji.sc/bugzilla/show_bug.cgi?id=744
Add special case for adjusting the position count when not grouping files
Merge pull request #1087 from melissalinkert/metamorph-performance

Metamorph .nd performance improvements
Merge pull request #1018 from melissalinkert/flex-naming

Flex: fix support for new file naming scheme
merge dev_5_0 -D org: PR 1078 (Lots of Zeiss CZI fixes)
merge dev_5_0 -D org: PR 1080 (Exclude log4j and packages from target-test-runner)
merge dev_5_0 -D org

Repository: openmicroscopy/bioformats
Already up-to-date.

Merged PRs:
  # PR 1078 melissalinkert 'Lots of Zeiss CZI fixes'
  # PR 1080 melissalinkert 'Exclude log4j and packages from target-test-runner'

Generated by BIOFORMATS-5.0-merge-daily#824 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-merge-daily/824/)