Update README

Update readme.

Explain more options for run_modules.py and process.py

```
time python python/process.py -j runs/submission_Run2_2020-09-20_22-43-15.json -r -p
```

Add -b flag to python/run_systematics.py... as in general we have to run with -b... or we could change the default.

Add explanation of more scripts.

