My shell script move change the location of the .git repo from localsite/themes/themename/.git to localsite/.git Note that when this script is finished you'll have to manually move the directories accordingly.

move-git.sh

#!/usr/bin/env bash

# set -x
# trap read debug

[[ $@ ]] || { echo "Please identify theme name" ; exit 1; }

if [ ! -d ".git" ]
  then
    echo "Y U no have .git directory?"
    exit 1
fi


GLOBIGNORE=".git:themes"
mkdir -p themes/"$1"
for i in *
  do
    if [[ $(git ls-files "$i") ]] 
      then
	echo "moving " "$i" " to themes/""$1""/""$i"
	git mv "$i" "themes/""$1""/"
      else
        echo "$i" "not in repo"
      fi
  done
unset GLOBIGNORE
mkdir libraries modules
touch libraries/.keep
touch modules/.keep

Need to add the .gitignore and .gitattributes to the root directory