Loghi Perinpanayagam, I think we didn't have an issue for this? If we did, feel free to close this one.
For others, the summary is that when running code with the interpreter, the kernel is executed using the Java process working directory.
We had some code that tried to change the working directory. But that worked only for Python. Magic commands like %%python do not work with every kernel, so we have to find another solution.