All buttons are commands. An Opus toolbar button contains at least one command, possibly even several (if they didn't, they wouldn't do anything when you clicked on them). Any place in Opus you see a button or a menu item, it's a command (called a raw command) that makes it work. You can edit each of these buttons and see the raw command that makes each of them work.
Exactly, this is not how it is supposed to work. You cannot drag buttons (which do contain commands) to the All commands list. None of us can, nor would we want to. Think about how you tell Opus what to do for you. You do not execute a command by clicking on the All commands list. You execute them by clicking on a toolbar button or a menu item.
The All Commands contains what are called Predefined Commands--they were built from raw commands and provided by GP Software to offer the most commonly required commands to new users. This way, a new user doesn't have to learn raw command syntax at first, since the most common commands have already been predefined as pre-packaged buttons. Consider the All Commands as the "default" buttons that have been pre-packaged to start you off. They are a subset of a much larger list of raw commands.
This isn't quite correct. You need to change your thinking here. Toolbar Button = one or more commands. Nero "burn Audio" is a command, but it is an external command--Nero is not part of Opus, but Opus can run Nero from inside a toolbar button.
You will not see it anywhere after that. This action is how you delete a toolbar button. This behavior is exactly the same as in some other applications that allow you to customize their toolbar and menus (like Microsoft Office applications for example). In these applications, and in Opus, you cannot drag commands from a toolbar to the commands list and expect to see them added to it. The command list is only displayed when you are in Customize mode, and dragging to the list only deletes the button.
This is purely coincidental. There are far more raw commands than there are icons to symbolize them. This is why a good toolbar button also makes use of a Name and Tool-Tip description to identify what it actually does.
Yes you do, but you have bigger issues to address first. I would get Opus working correctly on your system before actually customizing it further or playing around with File Collections.
Still, you should actually already have this command--it's just hidden. If you hover your mouse over the Delete button (with the big Red "X" icon) that came on the default Opus toolbar. You should see a tool-tip letting you know that it is actually a multi-function button. The left-click (LMB) command is the regular Delete which would destroy your folder or file when used inside of a File Collection. The right-click command (RMB) should be the Remove From Collection command.
The drag and drop (from All Commands to a toolbar) is the real issue here. However, since I cannot help you with this issue, I'll leave it for those more in the know about it. If it were me, I would rebuild my system over, or at a bare minimum use System Restore to roll back to a known working point. You have gnomes running around your system mucking things up, but I don't believe Opus is one of them.