Commands represent the core logic of the GPHUD - almost everything you interact with in GPHUD is just running a command, and by abstracting commands away from the implementation / interface, they can be invoked through different mechanisms.
There are currently 4 ways of running commands:
Interacting with the GPHUD directly - clicking a quick button or selecting a dialog menu item will cause the attached command to be run. If the command requires parameters, the 'template' will be dispatched to the HUD which will then prompt the user for the rest of the parameters before executing the command (validation permitting).
Executing commands through the “command line” - HUDs can currently be interacted with on channel 1, and the server its self responds to public chat that starts with the '*' character, so you can run /1character.status for example and will see the data about your HUD's connection, or *character.status around the server will tell you about its connection. Parameters should be specified, space separated, and if multiple words are required for a parameter it should have quotes around the parts, for example 'configuration.setzone “Some Zone” key.name value'
Through the GPHUD web panel - the bottom right button on the HUD will allow you to open a small in-game interface to the commands via a web page, enabling you to select more options via drop down lists etc
Through the web interface - most administrative functions are just exposed as commands even through the admin web interface
A list of commands and their parameters and required permissions can be seen through the Web Interface's introspection/api menu.
The 'operational context' of a command defines wether it runs as an avatar or a character - administrative functions use your avatar and avatar permissions while in-context operations generally require an active character to operate.