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Added a "run cycle overview" to documentation (#3455)

* run cycle overview
* adjust flow format
* add to table of contents
* code highlighting points of interest
* remove highlighting
* java code highlighting
* fix lint error
* language change. swap parse+exec for run
* use back-ticks for it + describe. uppercase title.
* invoked to executed
* add comment, make ui-generic, swap arrows
* Swap java back to js as highlighting the same

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