Fix deprecation warnings in plugin.xml

There were numerous (130+) warnings in plugin.xml over deprecated elements of the Eclipse API. Some were deprecated as of 3.4, which was Europa or Ganymede, circa 2008.

Like I hinted to in an e-mail that I sent to the mailing list sometime early 2017, using APIs that have been deprecated for so long is a risk, one that gets bigger as time passes by.

Before moving forward with fixing bugs and adding features, I'd rather get rid of most warnings, if not all. A cleaner code base will make my development easier, quicker and more consistent.

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