I am attempting to use the glossaries package with LyX, and have had only partial success. I've put the appropriate ERT into my document and created a short makefile which exports the LyX document to TeX and runs pdflatex and makeindex to generate the final pdf. This works well, but I would like a solution that doesn't produce quite as much clutter. Obviously there is built-in support for the nomencl package, but that appears to not have been updated in the last 5 years or so ( http://www.ctan.org/tex-archive/macros/latex/contrib/nomencl/) and it doesn't appear to do what I'm currently doing with glossaries.
Is there a way for me to export the LyX document (and the included images) to a separate directory, the same way I would create a build subdirectory when compiling software? Right now, it just appears that "lyx -e pdflatex" just creates files in the directories where the source files are. Even better, is there a way to have LyX run makeindex and makeglossaries for me, and produce the final pdf without the makefile? I've been using LyX 1.6.5 and svn trunk. Thanks, Steven