Hello Milan,
If you check out the example workflow and packages that are used in the custom message example here, you can see that the path passed to rosgenmsg is to the folder containing the message package folders. In other words, the example looks like this:
custom_msgs/
├── A/
│ ├── msg/
│ │ └── DependsOnB.msg
│ └── package.xml
├── B/
│ ├── msg/
│ │ └── Standalone.msg
│ └── package.xml
└── C/
├── msg/
│ └── DependsOnB.msg
└── package.xml
In this case, "A", "B", and "C" are your package folders. You would provide the path to the "custom_msgs" folder to rosgenmsg.
Since you are looking into regenerating all built-in messages, you can find more detailed instructions on this answer. The most important folder to regenerate would be the common_msgs folder, which contains most of the messages packages used in ROS.
In terms of TurtleBot3, the majority of it uses the common messages, but there is a separate turtlebot3_msgs package that you can add to your custom message folder if you want to use them.
-Cam
