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Improve the organization of the output directory

CAULK Robert requested to merge improve-output-dir into master

With large scale simulations, all the, *.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, *, 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:


Edited by CAULK Robert

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