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I have two issues:

  1. The figures/tables in my appendix are being labeled A.0.1 instead of A.1. I assume this is because of the convention in my document is chapter.section.#. How do I change this for the appendix only?
  2. My bibliography is being considered at a higher level than the appendices and it's noticeable in the ToC and the pdf hyperref structure.

See my example (Contains LyX document and .tex export)

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Great! Thanks for the tip. Any thoughts on why the bibliography is "including" the appendix? The page number of the bibliography in the TOC is better than any other page numbers and when you look at the bookmarks, you have to open Bibliography to see the appendices – Dominik Apr 23 '11 at 23:17
up vote 4 down vote accepted

Just change the line \numberwithin{figure}{Chapter} to \numberwithin{figure}{chapter} (chapter without capital C) and it should be fine.

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To clarify for newbies such as myself, the "line" should be inserted just after the first appendix header (so that only from that point forth it is changed). If you are using LyX you can do so with ERT just after the heading. – Dominik Apr 24 '11 at 16:52

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