Dealing with files in a project efficiently

Ideally, I'd like a lightweight project management to keep track of existing pages for a whole application. The current unorganized page management is tedious for average projects, in my opinion.
A typical website needs to mock several pages and the current way is too inefficient for me (I really like balsamiq, don't get me wrong, but this is pretty frustrating).

From the persistence point of view, you really only need a separate project file, on top of the existing structure. This file would allow to add/remove pages, their order and fold them. Note that the mockup format don't have to change at all (think about any basic IDE as example).

The project could simply show the mockup/folder list on a side, but not load any mockup automatically as it would eat memory needlessy.

Alternatively, you could open a directory as a project. You gain simplicity but loose some metadata control (eg, preferred order of pages).