Added support for appendices in the LyX layout and more page numbering logic.

The LyX layout now encapsulates the \appchapter.

The bibliography listing now automatically generates the label for
the endofpages page counter. This label is used for counting normal
text pages. The page numbering for appendices still depends on
\appendices and \\appchapters. The \eofapppages is automatically
added to the end of the document.