A more complex application that is derived from a combination of different modules or "sub-applications" will be easier to manage by separating each module (or sub-application) into a different project in Eclipse. Each of these projects can be checked in to a repository in a version control system to maintain a history of the modifications made to the application.
In this scenario, the programs in each project may have dependencies on programs and files in other projects and may not execute in a stand-alone environment. For these applications, it is better to "link" each ProvideX Project to an existing application installation so that as each source file is modified and saved in the Eclipse environment an updated version of the program is copied to the application folder. This requires that the folder structure of each ProvideX project be the same as the existing application so that the updated program files get placed into the correct location.
See the ProvideX Builder documentation about the Output Folder Properties for an explanation of the steps required to setup this process.