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added ability to enable custom compiler flags

Keefer Rourke requested to merge custom-flags into master

This commit allows tools to define arbitrary text inputs as options; simple safeguards had to be added in buildTool.js and programmingParser.py to:

  1. skip empty text arguments without crashing (buildTool.js)
  2. handle possibly malformed compilation flags, such as those which do not begin with '-' character (programmingParser.js)

Testing should be done before this branch is merged to master, but it would nice to have this merged this weekend.

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