extractVirtualFileSystemResources does not set correct permissions

[steve-s]

Context: this helper meethod provides a way to extract the whole virtual environment to real filesystem and then continue as usual with GraalPy accessing the real filesystem. This is the most compatible approach, because some Python native extensions bypass the Python IO and want to access filesystem directly, which also bypasses the GraalPy VirtualFileSystem.

Specifically venv/bin/python is not executable. We can special case for the few known executables in the bin directory or store the permissions in the VFS (probably in fileslist, but we should ensure that the code reading filelist can handle the previous format too if possible for backwards compat).