How do you add new files to a feature that have been deployed? Are there any gotcha's that you need to worry about?
The best way to do this, is feature upgrade. You change the version attribute on your feature, and either declaratively or in feature upgrade code do your changes, such as adding new modules.
Note that there is no OOB feature upgrade tools in SharePoint. You need to code it, for example in Powershell, or use Chris O'Briens tool from codeplex.