this is not a problem for the most part, and it may seem to be desirable, but it does not reflect unpackaging.
on unpackaging, files are put in a subdirectory (the name of the gwf). if these files are packaged, the gwf is generated in that folder, one level down from the original gwf.
so if a developer unpackages a gwf, edits the files, and repackages, they will need to copy the gwf into the parent folder (over the old one) manually if they want to run it.
this issue will be affected by how easy it becomes to select where games are played from and where they are packaged from and to. in any case it would be better to avoid multiple copies of a gwf and its contents in different subfolders.
actually this would largely be fixed by allowing the gamebrowser to open a game.lua if it exists without unpackaging a gwf (for testing only, NOT for normal play!!!) so that the developer does NOT need to repackage the game every time they want to test it.