Extracting a number of subdirectories into submodules

extract.sh

#!/bin/bash
set -v verbose
trap exit ERR

#I want to extract a number of submodules from a larger project.
#Also to preserve untracked files (e.g. lengthy data build products)

CWD=`pwd`
REPO_DIR="direction_discrimination_analysis"
SUBMODULES="mothballed_writing previous_draft newer_draft"
REMOTE_REPO_ROOT_ABS="peterm@pat.shadlen.org:writing"
REMOTE_REPO_ROOT_RELATIVE="../writing"

#ptools

for i in $SUBMODULES; do
    git clone --bare $REPO_DIR $i.git
    cd $CWD/$i.git
    git filter-branch --subdirectory-filter $i
    cd $CWD
    git clone --bare file://$CWD/$i.git $i-clean.git
done

for i in $SUBMODULES; do
    cd $CWD/$i-clean.git
    git remote rm origin
    git remote add origin $REMOTE_REPO_ROOT_ABS/$i.git
    git fetch #Gitolite will automatically create a repo here.
    git push origin --all
done

for i in $SUBMODULES; do
    cd $CWD/$REPO_DIR
    mv $i $i.old
    git rm -r $i
    git submodule add $REMOTE_REPO_ROOT_RELATIVE/$i.git
done

#then move over untracked files.
for i in $SUBMODULES; do
    cd $CWD/$REPO_DIR
    FILES=$(comm -13 <(find $i | cut -f 2- -d / | sort) \
        <(find $i.old | cut -f 2- -d / | sort))
    for j in $FILES; do
        if test -e $i.old/$j; then 
            #skip subfiles that were moved when their parent dirs moved
            mv $i.old/$j $i/$j
        fi
    done
    cp .gitignore $i/.gitignore
done