DS-2648-2 Fix bug and fix doubling up of argument

[jrwishart]

There was a bug that if a single entity is found in all inputs (documents), then the mapply function would simplify the data structure and cause an error. This has been fixed with SIMPLIFY = FALSE. Added a unit test to verify bug is fixed.

Also, passing the input file path to NERAnnotate is redundant since the input file path is set in the cnlp properties. Removed that string argument, added a check that the file parameter exists in cnlp.

[jrwishart]

Strictly speaking this is a breaking change (incompatible API) and warrants a version bump to 3.0.0 since calls to NERAnnotate have changed.

NERAnnotate previously required an input file string path of the form NERAnnotate("path/to/input.file"). However, this string argument is removed since the file path that CoreNLP uses is already stored in the java properties in the volatiles environment.

I only incremented the patch version from 2.4.2 -> 2.4.3 and updated flipTextAnalysis DESCRIPTION to require 2.4.3 since I updated the calls to NERAnnotate there also.

[mwmclean]

Please separate some of the tests in test-entity.R into separate test_that() blocks describing what each is testing.

[jrwishart]

Please separate some of the tests in test-entity.R into separate test_that() blocks describing what each is testing.

Done in 3f3a242