The idea of having one binary application, you open it, and have everything in there (like IDE) sounds good to me. But I also see that more and more tools combine a backend application (client CLI/daemon running in the background) with a rich frontend web application for GUI.
Even for a native desktop application, I do not exclude having a daemon running in the background or on a remote server. But the main question is, what's better for the user-facing part? Native Desktop or Web App?
Which one do you think is preferable for a better user experience?
not full speed of your PC,
not enough hotkeys,
no giant lists without pagination,
no confidence that new/old version of browser will not break something,
obstructions of using 100% of display without pressing F11
and, of course, no ability to work without Internets with no afraid to wipe off "offline first" part of application if pressing something like F5 or Ctrl-W.
A web application pros: no troubles with exotic architectures, no piracy (if we are talking about proprietary things), easy networking.