A big issue for me is using FlatPak for development tools. I have queried this in the past on this forum and not found a general solution, in fact I was not offered any constructive help.
I use VSCode for Dart and Go and I use Netbeans for java. I also use FileZilla to manage a web application that I develop on Clear Linux and deploy to a RaspberryPi on my local network.
I could not use VScode as a FlatPak. I had install it manually because the sandbox could not see the bin directories for Dart and Go. It was also not able to see the environment variables defined for Java, Go and Dart. In fact I struggled for hours to get it to work, using FlatPak overrides solved some issues but the results were inconsistent and could not be undone without re-installation (it really should not be this difficult!).
I also loaded FIleZilla but I cannot get FileZilla to use the system editor, gedit, because it it outside it’s sandbox and does not exist in FlatPak space. In fact I cannot get it to use any editor without throwing an error.
Netbeans could not find my JDK for the same reasons. I had to do another manual install outside of swupd and the software app.
This is a HUGE issue for me as these tools are effectivly broken in FlatPak form. I have asked on this forum for assistance but not received any. There MUST be a solution, I cannot be the only one, but I do not think I should have to spend hours trawling the web to find it. If FlatPak breaks these tools then the installation details should explain what to do to get plugins and external resources to work within the confines of the FlatPak.
How can you package tools that REQUIRE external resources in a FlatPak, it breaks the functionality.