Updated 1 July, 2019
Using in-game console commands:
You and your players can command the bot via the server console. You can use this to hide your command from public chat if your server is not hiding commands.
Use the console command pm followed by the normal bot command.
eg. pm /locations
If you are not allowed to use the pm console command, the server will tell you that your command was denied, but the bot will see it and will treat your command as if you had typed it in chat.
For all in-game console commands, the bot will only see that you used the command. It will not see the server's reply. Currently the bot will not react to you using any other console commands in-game.
Setting chat colours via in-game console:
The bot does not update its chat colours if you use the console to set them. The reason for this is to prevent the bot from reacting to its own console commands. I could probably make it work but it was causing too many issues for me so I opted to ignore console commands and require that chat colours be set via bot commands.