When manually resolving directory conflicts isn't a feature

[Stephen J. Turnbull]

Mary Gardiner writes:

 > I'm currently working on two documents in two branches doc-1 and
 > doc-2. Each contains a new directory not in the other branch.

I'm having trouble understanding what you're doing here.  When I was
working on my dissertation (which was pre-RCS, so my VC regime isn't
relevant), I had this structure

master/ -+- thesis.tex    # the book version
         |
         +- wp.tex        # the article version
         |
         +- Makefile      # controls everything
         |
         +- includes/ -+- notation.tex
         |             |
         |             +- latin.tex
         |
         +- ch1/ ------+- ch1.tex
         |
         +- ch2/ ------+- ch2.tex
         |
         +- nec/ ------+- brainstorm.tex

thesis.tex and wp.tex contained the "chapter-level" sectioning
commands, and then \input the text from the subdirectories.

Now, by running LaTeX in the top-level directory with TEXINPUTS set
appropriately I don't even need to mention the subdirectories in the
\input invocation, all the build products are in the top directory
that won't ever get removed, and the subdirectories are clean.  Of
course I also had a 'clean' target in the Makefile.

This may not be ideal for you, but it might be better than what you've
currently got.  It would also be possible to have a separate build
directory, but it might take a little fiddling.