Categories are simply LoneWiki’s way of interpreting a folder heirarchy. This provides organisational advantages both inside the wiki and for browsing the raw files in Windows Explorer.
Pages and categories cannot be duplicated (e.g. two pages of the same name cannot be held in two different categories), as the wiki iteself operates transparently to folder structure — a link to “Page” will find “Page” regardless of what category contains it, or will create it in the wiki root from whence it can be categorised.
Of course, if you don’t like categories, you can disable printing of category footers and go on like nothing’s changed.
There are also a number of under-the-bonnet fixes and tweaks to make LoneWiki much more robust.
Download the new version here.