git subtree subdirectory without index clashes

init.sh

git remote add -f upstream_lib1 /repo.source.git
git fetch upstream_lib1
git remote add -f upstream_lib2 /repo.source.git
git fetch upstream_lib2
git remote add -f upstream_sites /repo.source.git
git fetch upstream_sites

git checkout -b upstream_lib1 upstream_lib1/master # now  on upstream branch
git subtree split --prefix=lib1 --annotate="[lib1]" --rejoin -b subtrees/lib1

git checkout -b upstream_lib2 upstream_lib2/master # now  on upstream branch
git subtree split --prefix=lib2 --annotate="[lib2]" --rejoin -b subtrees/lib2


git checkout -b upstream_sites upstream_sites/master # now  on upstream branch
git subtree split --prefix=sites --annotate="[sites]" --rejoin -b subtrees/sites


git checkout master # go back to master
git subtree add --prefix=lib/lib1  subtrees/lib1 -m"merging lib1"
git subtree add --prefix=lib/lib2  subtrees/lib2 -m"merging lib2"
git subtree add --prefix=webroot/sites  subtrees/sites -m"merging sites"

update.sh

#!/bin/bash
set -x
git checkout upstream_lib1 # now on upstream
git reset --hard HEAD
git fetch upstream_lib1
git pull upstream_lib1 master
git subtree split --prefix=lib1 --annotate="[lib1]" --rejoin -b subtrees/lib1
git checkout master # go back to master
git subtree merge --prefix=lib/lib1  subtrees/lib1 -m"merged lib1"

git checkout upstream_lib2 # now on upstream
git reset --hard HEAD
git fetch upstream_lib2
git pull upstream_lib2 master
git subtree split --prefix=lib2 --annotate="[lib2]" --rejoin -b subtrees/lib2
git checkout master # go back to master
git subtree merge --prefix=lib/lib2  subtrees/lib2 -m"merged lib2"

git checkout upstream_sites # now on upstream
git reset --hard HEAD
git fetch upstream_sites
git pull upstream_sites master
git subtree split --prefix=sites --annotate="[sites]" --rejoin -b subtrees/sites
git checkout master # go back to master
git subtree merge --prefix=webroot/sites  subtrees/sites -m"merged sites"