[numpy_version]: Grep without semicolon was catching lines that were not due. Added a file with function ids and names

[remove_sbatch]: now magicCut can be run as a normal script: does not submit any job, no need for setup

[Issue#1]: Now takes time steps as input

[Issue#1]: Added arg parse

[Issue#1]: Start removing the setup_tool.cmd

I can not modify files in '/gpfs/projects/bsc32/cs_collaboration/BestIterationCutter/'. For the moment I'll use my folder.

Numpy version of the magiccut script. This avoids one of the calls to paramedir that, with large traces, can be time consuming.