In designing our LOCKSS repository and Manifests, we echoed the methodology of institutions such as ... who list the available journals on one page -- then when you click that link, you're taken to a list of the years for each journal -- and you continue to drill down to access the Archival Unit (as LOCKSS calls it). For journals, the archival unit may be a single issue or a complete year's content. In our case the Archival Unit is a collection.
All LOCKSS Manifests are named Manifest.html. The top entry-level one is at the top of the file system in the web-accessible LOCKSS folder. This one lists each of the holder areas, and links to those manifests.
All manifests besides this one are located in Documentation folders at the directory level where they apply. That is to say, each holder area (such as u0001, the Hoole Image Collections) has a corresponding subdirectory (u0001) containing a subdirectory named Documentation, in which there is another Manifest.html. This one will list the links to the image collections belonging to Hoole Image collections.
Each collection has a corresponding subdirectory. Thus, all content for the University of Alabama Encyclopedia (u0001_1831001) will reside in the /u0001/1831001 directory. A subdirectory there named Documentation will contain another Manifest.html. This one will list the links to all the archival content for this collection.
The ordering of this content Manifest is in layers: "Administrative Information" contains icons and administrative metadata. Other layers are "Collection Level Metadata," (Item level) "Metadata," "Transcripts," and "Content." The latter is where the links to the tiffs or wave files or other archival bitstreams resides. All other layers will contain links to versioned files, with the unversioned (and unlinked) copy residing in that directory understood to be the most recent copy for use purposes.
To recap, our LOCKSS Manifests support drilling down to the archival content, and reflect our file organization pattern. All but the top level manifest are created and updated by script.