Updates the logging system

[joaomcteixeira]

Redoing in a different way after comments in #97

Updates and cleans the logging system.

• added complete control to where the logging messages are saved
• standard output is saved to stdout. Before it was saved to stderr because of the default value of StreamHandler. This is noted mostly when running SBATCH
• error messages as saved also to stderr
• logging is saved in file log inside the run folder.

I needed to do a quick trick to keep the logging in stdout and in the log file to accommodate the first steps during the configuration reading. Basically, messages are reported to stdout and to a StringIO until the log file is defined. After that, the buffer in StringIO is saved to the log file, and the logging continues normally after that. See clis/cli.py.

This PR does not clean the logging messages per se, nor does it adds progression bars as discussed in #97. Instead, this PR just updates the logging system itself. These other functionalities will be built on top of this and will be submitted in other PRs.

[amjjbonvin]

Seems fine to me - the logic makes sense.
But git report conflicts that need to be resolved manually

[joaomcteixeira]

Yes, now gives the expected output (not file size), running with sbatch on tintin:

 1 -rw-r--r--. 1 joaomctx users     0 Nov  5 14:03 hd3_scoring_err
 9 -rw-r--r--. 1 joaomctx users  4091 Nov  5 14:03 hd3_scoring_out