The first time that a repository administrator opens the JS Hooks page for the repository they'll be prompted to enable JS Hooks for the repository. This will enable the repository hook automatically. If for some reason the Repository Hooks are disabled through the Hooks screen, the administrator will be repromted.
Writing a Javascript hook
Writing a Javascript hook is quite simple. Simply click on "Add Hook" on the repository JS Hook page and you'll be presented with a screen for your editing. Each Hook will require a name and the script itself.
As part of the editing experience, you can select a changes (or a pull request in the case of a merge check) to run against. This will run your actual Javascript code against the particular item as if it was "live". At the end of the run you can see if there was an error with your code and which of the external api calls were called (and what the arguments passed to them were).
Once saved - the hook becomes active. At any point though, you can disable the hook from the repository view page.