Now I've updated it, but I have a feeling this is gonna be deprecated.

Maybe I'm wrong, but shouldn't this be entirely replaced by ayatana-indicator-application?

Yeah, you're right. Good catch.
Admittedly I didn't put much effort on this package because I'm not sure about what requires it. MATE should require it, yet no package is a revdep of indicator-application, so I wouldn't even know how to test ayatana-indicator-application...

@JoshStrobl thoughts? Should ayatana-indicator-application replace indicator-application and hope all will work?

You know what? Gonna download the MATE edition, uninstall indicator-application from it and see what happens.

What I discovered:

• the indicator-application systemd service is not running on a fresh installation
• I added one "Indicator Applet", one "Indicator Apple Appmenu" and one "Indicator Applet Complete" to a new panel. They work (although I think they use mate-indicator-applet). Tested with workrave
• I ran sudo eopkg rm --ignore-dependency indicator-application and rebooted
• Everything works as above. I also installed telegram to test the classic systray. All good.

So I think MATE moved to its own fork/implementation of indicator-application.

A-ha! Using lsof it turned out that mate-indicator-applet actually reads .so files provided by indicator-application. Source code confirms this: https://github.com/mate-desktop/mate-indicator-applet/blob/master/configure.ac#L201

I have no idea why mate-indicator-applet works correctly even without that library files, but I think we now made the situation clear: mate-indicator-applet should depend on libayatana-indicator-application.