Began adding JavaDoc comments

This commit adds JavaDoc to the Glyph class, has the barest start to
documenting the Grid interface, and brings in a great many generated HTML
files.
More JavaDoc comments

Added comments to Grid. Fixed a broken link in the Glyph comments. Removed the
generated docs from repository and set them to be ignored in future.
More JavaDoc comments.
More classes given JavaDoc comments.
JavaDoc comments added to more classes.
Added JavaDoc comments to the DigitTransition class.
Improved the JavaDoc comments in a number of classes and interfaces.
Progress notes updated.
Renamed DigitTransition to GlyphTransition

DigitTransition was an accurate name because currently only digits are defined
using the data structure used by the makeTransition method. But what it does
is not specific to digits. I renamed it to suit the intended purpose.
Added JavaDoc to DotChangeAction
Small JavaDoc comment accuracy improvement.
Renamed the Glyph member

I renamed the Glyph member to better indicate that this can be targetted at
any kind of Glyph, even if the current implementation only ever updates
Digits.
Added and improved JavaDoc comments in many classes
Add and improve JavaDoc comments - first pass over all code files now complete.