Use literal_emphasis node to render CLI command and prepend omero

Following a discussion with Helen, we decided to now use the default_role to
mmarkup commands instead of the :command: role.
Review all occurences of command and omerocmd across the doc

- omerocmd role is now completely OS independent and :omerocmd:`command subcommand` now displays as  omero command [subcommand]
- when paths are needed, command/omerocmd are converted using file markup, e.g. :file:`bin/omero`
- all other command are marked using the default role, e.g. `command`
Preprend omerocmd index entries with "omero" for clarity
Update Readme to document command/omerocmd formatting changes
Use literal role instead of default role when displaying commands
Additional command fixes noticed by Helen
Merge pull request #249 from sbesson/rebased/develop/command_formatting

Command formatting (see #10213) (rebased onto develop)