I need to install a app to a folder outside the program files folder.
into the root of a drive to make it portable.
Like to c:\appfolder.
how can I get the JPE to recogize the files install into that folder.

Yes, it is possible to make portable that is not installed into Program Files folder. But it will not be easy as JPE Quickie or JPE Setup Capture.

In order to do that, use The 12 Step Program method. When you come to the step of editing configuration ini, add the non-special folder path in the [FilesystemInclude] and [SpecialFolders] so that JPE recogize the files install into that folder. For example

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JauntePE the portable maker: <<JauntePE Google Site >>

Thanks now I have something to test with.