It seems you have gotten the impression from somewhere that everything should go into one single program. This is not the case. You probably haven dozens of different programs and file formats and physical storage.
For example, everything that you keep for possible future use, whatever it is, is called Reference in GTD. You probably have some of this on paper, some on a computer, some on a disk etc etc. Of the computer stuff, some of it is .jpg, some is .docx, some is .xlsx etc etc etc, some you keep in Evernote, OneNote, DropBox, Google Drive etc etc, some of it is your email archive, and fax/paper correspondence archives. You probably will not reorganize all of this just because you now use GTD, but you want to make sure you can find what you need in it
GTD is primarily concerned with actions, projects (and areas etc - six horizons). You can either keep these lists on paper, as described in the book, or use a paper-emulating list app, such as Wunderlist, Google Tasks, iOS Reminders etc, or some more advanced (cross-referencing) app (such as Toodledo, Omnifocus, Things, Nirvana, Doit, Zendone, GTDNext etc). There are advocates here for all those three approaches. Personally I used paper for 20 years and thereafter computer for nearly 20. I prefer the more advanced type of app; I see no point for me personally in using a simple paper-emulating app like Wunderlist and I would not "build my own thing" either (using some general tool like Evernote, Excel, Workflowy etc).