Combine multiple documentclasses; maintain page numbering and structure for TOC/TOF

I'm writing a thesis that includes two articles. The institution provided a style file for the thesis; the articles use IEEEtran. Furthermore, the used packages in each document may differ significantly.

Desired Result: a single PDF that contains the thesis and articles while maintaining each document's prescribed format and consistent page numbering. The PDF should also include a single comprehensive table of contents (TOC), table of figures (TOF), table of tables (TOT) and bibliography. This document document would be structured as follows:

• Front Matter (e.g. Title Page, TOC,TOF,TOT, Abstract)
• Introduction
• Article 1
• Article 2
• Conclusion
• Back Matter (e.g. Bibliography)

The combine package would not compile the document. The pdfpages package was able to build a single, combined document with consistent page numbering, but I am unable to produce the TOC/TOF/TOT/Bibliography. Can anyone provide a minimal example of a working solution?

• If the articles have their own section information, etc. you can use the pax package with pdflatex or lualatex to include that information when the pdfpages package is used. – darthbith Jan 12 '16 at 15:05
• can you add informations about Bibliography? why this is a problem for pdfpages? – touhami Jan 12 '16 at 16:21
• The bibliography in the back matter should include all references from all documents. I may be able to just whittle the *.bib file down to only those references that were cited and use the \nocite{*} command in the back matter, but the real challenge seems to be getting the TOC/TOF/TOT working. – Austin D Jan 12 '16 at 16:34

Here is a solution

\documentclass{book}
\usepackage{blindtext}

\usepackage{pdfpages}

\begin{document}
\tableofcontents
\listoffigures
\listoftables
\blinddocument
%-------------article1
\clearpage
\includepdf[pages=1-2,pagecommand={bla}]{myfile2.pdf}
\clearpage
\includepdf[pages=3-,pagecommand={bla}]{myfile2.pdf}
%-------------article2
\clearpage

Take the bodies of the documents, put them into separate files, which you \input{...} (or \include{...}, if separate chapters, which start new pages) from the main file.