Just a tiny note: I got a "safe mode, limited functionality" warning in pycharm. It just did not want to go away, not matter what I tried.
Solution: the file ~/.config/JetBrains/PyCharm2021.3/options/trusted-paths.xml contained
<entry key="$USER_HOME$" value="false" />Setting this to true or removing the entry solved my issue.
The reason for this unwanted behaviour was that I opened a file in my home directory using 'charm', and marked that as untrusted. This seems to have applied the entry, and the gui did not allow me to remove it.