Andy McFadden 22c47e1d0b Update reference manual formatting ...

Switched from XHTML to HTML5.  Added formatting for menu items and
keyboard shortcuts.

Made various minor edits to the text.

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advanced.html

Update reference manual formatting

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analysis.html

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codegen.html

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editors.html

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end-notes.html

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index.html

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intro-details.html

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intro.html

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main.css

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mainwin.html

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settings.html

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tools.html

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tutorials.html

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visualization.html

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