Fix CLI tools when used from a source working copy

There is no longer a bio-formats.jar. We can use formats-gpl.jar
instead, which references the others in its manifest Class-Path.
Add missing dash
Update build script to correctly pass Sphinx options to Ant
merge dev_5_0 -Dorg -Ssuccess-only: PR 1281 (Update release notes for 5.0.4)
merge dev_5_0 -Dorg -Ssuccess-only: PR 1298 (Fix CLI tools when used from a source working copy)
merge dev_5_0 -Dorg -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1282 melissalinkert 'Update version numbers to 5.0.4' (label: exclude)
Updating 077b4bf..3faf90c
Previously merged:
  # PR 1294 sbesson 'Add documentation for PicoQuant .bin format'

Merged PRs:
  # PR 1281 melissalinkert 'Update release notes for 5.0.4'
  # PR 1298 ctrueden 'Fix CLI tools when used from a source working copy'

Generated by OME-5.0-merge-push#205 (http://ci.openmicroscopy.org/job/OME-5.0-merge-push/205/)