Create pdf from tex files with the table of contents and other lists included, since pdflatex will be invoked twice. You'll only get the pdf, not any other output file.

pdflatex+

#!/bin/sh
# 2014 CC0 http://creativecommons.org/publicdomain/zero/1.0/
# Create pdf from tex files.
[ $# -lt 1 ] && echo Usage: $0 tex-file && exit 1
OUT=/tmp/pdflatex+out
[ -d $OUT ] || mkdir $OUT
PL="pdflatex -file-line-error -halt-on-error -output-directory $OUT"
for file in "$@"
do [ -f "$file" ] && $PL -draftmode "$file" && $PL "$file"
done
mv $OUT/*.pdf . 2>/dev/null