The default LATEXoutput is a file for each of the source files with one extra file ``cxref.tex'' that includes each of the other files. This is to allow a makefile to only update the changed files (although the references may require all of the files to be checked again). When the cxref.tex file has been written it can be modified by the user, any new files that are added are added at the end of the source code section, the rest of the file being unchanged.
The index is written to a file called ``cxref.apdx.tex'' and cxref.tex is updated to refer to it.
Also written out are three LATEXstyle files ``page.sty'', ``fonts.sty'' and ``cxref.sty''. These set up the page to use a smaller margin and smaller fonts to allow more to appear on a page and also define the new commands for typesetting the cxref output.
(The file names ``cxref.tex'' and ``cxref.apdx.tex'' are different if the ``-N'' option is used.)