Restructure planemo commands

Running `planemo --help` is quite intimidating for a new user. It would be good to organise the subcommands into groups, e.g. all the `conda_*` or `training_*` commands under a single umbrella. The help would be much more concise as it would only show the higher level commands; more detail could be obtained by running e.g. `planemo training --help`.

Likewise running `planemo test --help` returns more than 70 different options, most of which the average user honestly doesn't need to care about. Perhaps some of the commands could be hidden and accessed via something like `--full-help`.