tr improvement + dojo-like output

[maxaalexeeva]

• tr improments from @maxaalexeeva, @alicekwak, and @sarahstueve

Major changes:

• a script to jointly extract mentions from papers and markdown files related to one model and assemble them into a json object similar to that produced by dojo api
• location and date rules
• rules and methods for command extraction and assembly of command sequences from command components extracted with rules
• adjusted python script for querying HomeController endpoints

Minor changes:

• new and adjusted rules
• rearranging taxonomy and master ymls a bit
• storing file names in location attachment
• disallowing cosmos block merge if content starts with a digit---those are frequently just section ID---that is the start of a new section
• fixing a special char remapping bug
• added some methods for cross sentence event mentions
• adding color to commands in the visualizer

[codecov[bot]]

Codecov Report

Merging #278 (7c2dbb1) into master (04b883a) will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #278   +/-   ##
=======================================
  Coverage   66.04%   66.04%           
=======================================
  Files          95       95           
  Lines       17892    17892           
=======================================
  Hits        11816    11816           
  Misses       6076     6076           

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[maxaalexeeva]

hey @alicekwak, I added int param setting output to the mention assembly json in response to your question and also modified a couple of python scripts that are supposed to run some of the endpoints in HomeController. I think I will stop with this branch modifications now :)