I didn't find anything mentioning this specific issue online so I thought I'd make a short article to help anyone in the same position. This should be relevant to anyone who has installed Intellij-Idea (or any other Jetbrains app) within a sandbox environment, such as Flatpak or Ubuntu Snap and is having problems accessing files from their system through Intellij.
Problem
I installed Intellij-Idea on my Pop!_Os Linux (A fork of
Ubuntu) setup through the Pop!_Shop, which typically installs the apps
as a flatpak file. I was having strange issues where Intellij-Idea
wouldn't list all files under certain directories, such as /usr/bin.
In my case /usr/bin/bash was visible and selectable, but not
/usr/bin/zsh.
I tried various things to get this to work as well as searching for
anyone who had run into the same situation. I ended up setting up a
separate .bashrc mimicking most of my .zshrc for Intellij-Idea
itself.
I was trying to find a quickfix instead of trying to figure out what was
going on. Today I wanted to get it to work since I wasn't able to export
my local DB through pg_dump, since /usr/bin/pg_dump was one of the
binaries not there.
I realised that it was installed as Flatpak app, which runs in a sandbox and must not have some or other permission. I tried installing Flatseal to give the permissions. Unfortunately I wasn't able to give Intellij-Idea the necessary permissions. I'm really glad I came across Flatseal though, it looks like a great tool.
Solution
To make sure there weren't sandbox permission issues, I installed the Jetbrains toolbox app via the instructions on the Jetbrains website. The standalone install would work too.
This solved all of the app permission issues I was having.
While I had this issue with Flatpak, I suspect this would be an issue on Ubuntu if installed as a Snap package.