>It would be nice to be able to flag files in the Project Manager somehow that are currently under development. Is there a way to do this or maybe develop a hook to do it? I may have anywhere from 1 to 15 or so files of different types, related by whatever current development project/issue I'm working on. Would be nice to be able to group them somehow.

Take a look at the Component Gallery. You can create a folder with references to those files that must be worked on as a group. Too bad it can build a project.