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A simple convention is used to locate and place the individual files used in a multi-source document. Basically, the "included" files are placed in a subdirectory with a .dir extension, however the including file is kept at the outer level. This scheme has the advantage so that if a single-source file later becomes split up, the "including" file itself does not move so you always find it in the same place.
So, as an example, we have a A Guide to Synthesis Processing in AIPS++ under the code/doc/user directory. We call it synthesis.latex. At a later point we might want to split this document into multiple .tex files for convenience, or we might have some .ps files. In this code we would make a directory code/doc/reference/synthisis.dir and place those files within it, however synthisis.latex would remain in code/doc/user.