A Bash function to strip %-style LaTeX comments. The script correctly treats escaped percents, and comments after double backslashes.

strip_latex_comments.sh

# Usage:
#   strip_latex_comments file.tex file.nocomments.tex
#   strip_latex_comments_inplace file.tex

function strip_latex_comments {cat "$1" | '"sed 's/\([^\\]\|^\)\(\(\\\\\)*\)%.*/\1\2%/g' "'> "$2"; }

function strip_latex_comments_inplace {find . -name '*.tex' -exec sed -i'' 's/\([^\\]\|^\)\(\(\\\\\)*\)%.*/\1\2%/g' {} \; }

alias stip_latex_comments2="sed -e 's/\([^\\]\|^\)\(\(\\\\\)*\)%.*/\1\2%/g'"
# strip_latex_comments2 file.tex > file.nocomments.tex

function strip_latex_comments_inplace2 {sed -i'' -e 's/\([^\\]\|^\)\(\(\\\\\)*\)%.*/\1\2%/g' $(find $1 -name '*.tex') }
# strip_latex_comments_inplace2 mytexdir