@(zackadelic, jangell2): (no, no).
Ok, so I took a further look at the 5.4.2 issue, and here's the outcome:
There are two separate problems.
The first problem is that there are now two kinds of collections, namely cloud collections and local ones. This is relatively easy to solve -- or at least to work around -- by having CM ignore cloud collections and only operate on local ones (which is what it's currently doing anyway).
The second problem is much more fundamental. Before 5.4.2, database entries which had the "isVisibleInHome" attribute set to "0" were simply not shown on the
home screen, but were otherwise treated as fully functional entries. CM used that property for nesting, which resulted in an organization that could simulate a hierarchy. Starting with 5.4.2, entries with that attribute set to "0" are not considered
at all anymore. In other words: they are not displayed at all, anywhere. They are still "physically" present in the database (which is why they are still counted when asking a collection for the member count, and they can even be modified in CM to be visible again), but they don't show up when asking a collection for its members. This explains the weirdness both in the native UI, and in CM itself.
The bottom line is:
with FW 5.4.2, hierarchies essentially became impossible. Or, more accurately: it is still possible to create multiple paths to access an item (by nesting collections). But all those paths will be visible on the home screen, thus making a hierarchical organization pointless.
Well thank you, Amazon, for another update that makes the Kindle even less usable.