Class Hierarchy view: add an option to show top level deprecated classes
With the availability of bulk operations such as "Set annotation value..." and "Edit annotations..." one can set the deprecated flag for several top level classes at once. With the changes introduced for #395 those top level classes that have their deprecation flag set would simply disappear from the tree (and to be more confusing this happens not right after the bulk operation, but only after the tree is refreshed), which may take the user totally by surprise and let him/her confused or panicked about where their classes disappeared. Moreover, even if they would figure it out that their classes may have disappeared because they deprecated them, in the absence of any easy mechanism to gain access to them, it would be very difficult for them to un-deprecate those classes again.
Therefore, to me it seems critical to provide an option (ideally to the "Class Hierarchy" view) to allow the user to see the top level deprecated classes as well.
See also #406
This is an important feature. Not all projects want the deprecated top-level classes to be hidden. This should be a configurable option. The default can be to hide them, but a project owner should be able to show them, if necessary.
I would argue that most projects do not expect the top-level classes to not show at all. Also, the class tree should give some indication that there are hidden classes.
See the deprecated entities view in the mean time
More on this. I think adding a link at the bottom to say, "there's deprecated classes that aren't shown here", which would then show them (somewhere) is a good idea.