Just wondering: Would the following be difficult to implement in Lyx or to use it via enter>file> 'external material' ?
Wolfgang From http://ctan.tug.org/tex-archive/help/Catalogue/entries/texdirflatten.html Collect files related to a LaTeX job in a single directory. The Perl script parses a LaTeX file recursively, scanning all child files, and collects details of any included and other data files. These component files, are then all put into a single directory (thus “flattening” the document’s directory tree). The author is Cengiz Gunay.