Improve the organization of the output directory

With large scale simulations, all the client.X.sh, *.err/out files are written to the top of the output directory. This makes it quite difficult to navigate for locating important unique files (*.log, *_server.py, config*.json etc.).

Here we redirect all client scripts to output_dir/client_scripts and all *.err/out to output_dir/stdout.

Here is the structure: