Implemented unified log file to improve state-tracking and categorize output files

[guechhouth]

Summary

1. Implemented unified log file (snakemake-rules.log) so that newly submitted step jobs can be tracked without having to run condor_watch_q again.
2. Implemented Andrew's feedback -- one directory (nested in the logs) per rule name.

• The format is: logs/RuleName/RuleName_Snakemake's JobId-ClusterId.err, logs/RuleName/RuleName_Snakemake's JobId-ClusterId.out.
• RuleName_Snakemake's JobId-ClusterId is what shown exactly on the status bar when running condor_watch_q.
• Management-related files and snakemake-rules.log will be directly under logs/.

Limitation

• Currently, newly submitted jobs will be shown on the status bar under the Batch as ID: ClusterId instead of its actual rule name unless condor_watch_q is called again. This likely has to do with how condor_watch_q operates. Hopefully, this can be fixed once Cole has done working on HTCONDOR-3656.
• The tests in tests/ are failing since they might not have new attributes.