I didn't see it, so figured I would add my two cents worth.
The easiest way I found to do this is to just re-add the library folder (without deleting the library because that is time consuming and unnecessary) for example.
Although i Tunes lets you “manually manage your library”, it’s never intended to let you move things around in the filesystem, add, remove or modify files.
On the other hand, it simplifies a lot of things for a lot of people. If i Tunes had to scan the filesystem for changes every time it ran, the program could potentially slow to a crawl.
I also have "Manually manage music" selected for my ipod, but I don't think that's related to how I store my music.I changed the location of my i Tunes library in preferences.Then, I selected all songs in i Tunes and deleted them (they didn't delete off of my original library location).It always adds the new movies I've put in the i Pod Movies Folder.It is still a manual process, but it is quick and it adds all movies I've added since the last time I did this, and it is free and doesn't use up memory running in the background (unlike the albumbrowser recommended above).I keep my music on an external hard drive, and whenever I add new music to it, I go to File - Advanced) unchecked the "Keep i Tunes Media folder organized" and "Copy files to i Tunes...".