Generally not everything is going to work through Commandr. Certain tools are best done via a web interface because of the need to stream a download or interactivity or being integrated also via AJAX. Certain tools are best done from SSH due to long run time, or needing special permissions, or potentially breaking the site (so needing running outside it).
We now have the professional upgrading tutorial which provides a great deal of advice.
Also the codebook provides an index of tools.