Flatpak isn’t really meant for this scenario. Period.
Let me try and explain why we have flatpak - about 2-3 years back, Clearlinux had very little end user GUI applications. We knew already it was going to take us a very long time to package many of these and even the, some are just things we can’t ship for various reasons (proprietary etc.). However, it instantly gave every clearlinux user access to almost 300 applications. That allowed us to focus on things like the overall GUI, installer etc. and make more progress in other areas.
However, many software programs don’t make much sense to run in a restricted sandbox and they need access to outside resources. Flatpak has the problem that it’s not really possible to export multiple binaries into a flatpak, and device node access and drive access is difficult at best. For things like media players, it’s relatively simple because “videos” is a known export. But for things like “Java development workspace” there is no equivalent XDG export directory, and nobody puts these workspaces in “Documents” either. So essentially all flatpak IDE’s are broken.
The proper solution is that we add these IDEs one by one as bundles to Clearlinux. You can request these by filing a ticket on our github tracker. Some IDEs are already bundled, and, we’ll do our best to add new ones especially if they’re widely used.
(Why does the forum mangle this link? It’s a link to our issue tracker)