In order for Neptune to reload a component, you must let it know that the component has been changed. You can do this by adding a "refresh" URL variable to the request.
For example, if you changed Application.ContactOMatic, you would go to ?refresh=ContactOMatic in order to reload it. This will reload the specified component as well as any component that it is passed into (directly or indirectly).
The "refresh" value can also be a list of components. So, if you wanted to refresh both Application.ContactOMatic and Application.HR at the same time, you would use ?refresh=ContactOMatic,HR. Of course, if either of these is passed into the other than specifying the other is redundant (but harmless).
Neptune should automatically detect any changes to simple configuration variables (non-complex variable types) passed in to components for initialization and automatically reload the appropriate components. It will not, however, be able to detect changes to complex variables (structs, arrays, etc) passed in to initialize components. If you change those, then you will have to use the "refresh" query string as above.
Although you would not normally need to do this, you can also refresh everything by using ?refresh=true.
If you want Neptune to check for new components, but not refresh any existing components, then you can set refresh to any value other than true, false, or any component name. By convention, "any" is usually used for this purpose: ?refresh=any.
You can change the value of the URL variable used for reloading components by editing /_config/invoke.cfm and replacing any instance of "refresh" with the variable name that you wish to use instead.