Add sudo functionality to the sysadmin CLI documentation
Expose -h option as the entry point for sysadmins/developers
Add minimal information about -f/--depth argument of bin/omero import
Add documentation for the CLI obj command
Expand setup.py test/py.test options description

- Use sphinx option markup for clarity/cross-referencing
- Put -h/--help at the top of the option list
- Add description for --markers option of setup.py test
- Add description for --repeat option of py.test
Implemented fixes suggested by Colin
Merge remote-tracking branch 'origin/dev_5_0' into 5.0.3_cli
Slightly expanded re-indexing intro
New CLI reindex commands
Clarify *when* to re-index
Migrate troubleshooting text to search.txt
Add note about fewer results during indexing
Fix indent in bullets
Clarify that FileAnnotations are not under 'annotation:'
Replace broken links with TODOs
Unify option description
Fix typo
Suggested improvements from Petr
More improvements of why corruption can occur
Handle double hyphen with mem