Updated 2 July, 2019 (work in progress)
By default the bot uses / infront of commands but you can tell the bot to use something else. Also you can just talk to the bot and a small number of commands can also be typed without the command symbol (slash).
When the bot first joins a server it will send some commands to the server so that the bot can learn various things such as the settings in the server config, the list of admins, bans, the zombies, items and players known to the server. Some of these lists are quite large and the bot may become unresponsive for a minute or two. Once it has gathered and processed these things it won't need to grab such a lot of data again. There are commands to force it to send them again such as /fix bot. The bot requires that Alloc's mod is installed or several important console commands (mainly pm) will be missing which will prevent the bot from private messaging players. With no mods installed the bot will sort of work but will seem broken. In order to have all bot features available you also need to install StompyNZ's Bad Company (BC) mod. See the download page for links to the mods.
With the BC mod installed you can do a lot of cool stuff. One ability you will want is to hide commands from public chat. To do that type /hide commands. You can also add trader protection, automatically despawn zombies, dig big holes (or fill them), replace blocks in a defined area with another block, despawn traders and other entities, turn on lights and close doors, and lots more.
Sometimes there can be a few teething issues with the bot when it first arrives. To avoid most of them there are some commands you can use to give the bot a bit of a nudge. They are /reload bot, /restart bot, /fix bot, /update bot, /reload code, and /reload admins. There are more commands but one or more of these should help fix any bot issues so long as the cause of them isn't an issue with mods not being properly installed or something else beyond the bot's control.
The bot has many features. I will discuss the major features here and this guide will be added to over time. Another good place to learn about features is in the various commands pages. For the moment each commands page just lists all of their commands and the command help for each. I will be writing some general notes at the top of each commands page focusing on the feature that they represent.
The topics and features that I will cover here are player bases, locations, villages, teleports, waypoints, security, the shop, reset zones, important bot, admin and server commands and the basic day to day stuff that you would typically do with the bot.
General Stuff
Important Bot, Admin And Server Commands
Feature: Player Bases
Feature: Locations
With the bot you can divide the world up into zones, create locations and teleports. If your server is PVE there is a special location you should create somewhere called prison. If you do not have the prison location and a non-admin kills another player, they will be temporarily banned. With the prison location existing, they will be sent there instead and admins or the player they killed can release them. Prison and indeed all locations have many settings. You can set up the prison to have a timer or set a bail or both. There is a special class of location called a village which acts like a player base but many players can be members (villagers) and one player can be mayor. The mayor can add and remove players as villagers.
Feature: Villages
Feature: Teleports
Feature: Waypoints
Feature: Security
Feature: The Shop
Feature: Reset Zones