Script to prepare arXiv package of a document that depends on texlive2014's version of biblatex (http://biblatex-biber.sourceforge.net/).

make-arXiv-package.sh

#!/bin/bash
#
# This script is useful if:
#  - you have a manuscript that you want to upload to the arXiv,
#  - you are using biblatex, and
#  - you are using texlive2014 while arXiv is still on texlive2011
#
# Put this file in a directory containing the manuscript you want to
# upload to arXiv.org, and adapt the paths below.


# The main latex file of your document (without .tex):
MAIN=main

# You must have both texlive2011 and texlive2014 installed:
TEXLIVE2011=/usr/local/texlive/2011
TEXLIVE2014=/usr/local/texlive/2014

# Adapt these paths to your texlive2011 installation
# (especially $PATH in case you have a 32bit system)
PATH="$TEXLIVE2011/bin/x86_64-linux:$PATH"
MANPATH="$TEXLIVE2011/texmf/doc/man:$MANPATH"
INFOPATH="$TEXLIVE2011/texmf/doc/info:$INFOPATH"
TEXMFHOME="$TEXLIVE2011/texmf"
TEXMFCNF="$TEXLIVE2011/texmf/web2c"

# This should point to the biber or bibtex executable of texlive2014:
MAKE_BIB=$TEXLIVE2014/bin/x86_64-linux/biber


if [ ! -d "$TEXLIVE2011" ] || [ ! -d "$TEXLIVE2014" ]
then
  echo "You must have texlive-2011 AND texlive-2014 installed"
  exit
fi

# make a temporary directory "arXiv-package" and
# copy texlive2014's biblatex there
rm arXiv-package.zip
rm -rf arXiv-package
mkdir arXiv-package
cp *.sty *.tex *.bib arXiv-package/
cp $TEXLIVE2014/texmf-dist/tex/latex/biblatex/*.* arXiv-package/
cp $TEXLIVE2014/texmf-dist/tex/latex/biblatex/bbx/*.* arXiv-package/
cp $TEXLIVE2014/texmf-dist/tex/latex/biblatex/cbx/*.* arXiv-package/
cp $TEXLIVE2014/texmf-dist/tex/latex/biblatex/lbx/*.* arXiv-package/
cp $TEXLIVE2014/texmf-dist/tex/latex/biblatex-ieee/*.* arXiv-package/

./git.tex.sh > arXiv-package/git.tex

cd arXiv-package

# Run texlive2011's latexmk, but without bibtex/biber
latexmk -bibtex- $MAIN

# Run texlive2014's bibtex/biber
$MAKE_BIB $MAIN

# Run texlive2011's latexmk again, but without bibtex/biber
latexmk -bibtex- $MAIN

# Remove files that arxiv does not want
rm *.aux *.bib *.blg *.log *.pdf

cd ..
# Create .zip archive
zip -r arXiv-package.zip arXiv-package
rm -rf arXiv-package

Thanks very much for putting this up. It really saved me a lot of time!
I made a fork with minor changes for a document using pdflatex (some extra files to remove and don't want to remove pdf figures)