I'm in the process of converting over all the commands to the new format.
All commands will start with !ct and as an example for adding a condition to a token:
!ct --add,condition=prone,duration=2,direction=-1,message=whatever.
All conditions will have a default message and there will be a configuration option to not use messages at all so the roll query for messages will or will not show up when assigning a condition for those who do not use messaging
I'm working with theAaron right now to integrate CT with tokenmod and the new tokencondition as well as groupinit. He may need to make a few minor changes to support this. A lot of people use group init, so enabling that API to roll init instead of the internal CT process will support those users. Roll20 is changing it's status/icon processing for custom icons, I can leverage tokenmod and tokencondition (either/both) to support that. Finally I'm putting stubs in for tokenmod so you can call it when assigning or removing tokens, such as moving a token to the GM layer upon death, etc.