The issue
whether the config.general.show_nested_entities flag is True or False, there seems to be no effect to the output.

Example
if the text is “chest pain” which matches 1) “chest pain” greedily 2) “chest” 3) “pain”, it seems to produce all 3 entities at the end at all time regardless of the flag.

What's wrong

• the current logic in postprocessing.py doesn't seem to be filtering anything.
• the filtering logic doesn't appear to look at the flag at all.

The fix

• re-implementation of the filtering logic to simply use token index to filter.
• the flag is passed on and checked during post-processing.