Modify Git repo history so that any files/folders not present in the current worktree when the script is run will be retoactively erased from history.

git-filter-to-current-tree.sh

#!/usr/bin/env bash
####################################################################
# Removes any files that are not currently in the working tree from
# the git repository history.
####################################################################

KEEPFILES=$(mktemp)
FULLLIST=$(mktemp)
REMOVEFILES=$(mktemp)

# Find all files in the current worktree:
find . | sed "s|^\./||" > ${KEEPFILES}

# Discard any unstaged changes
git reset --hard

# List all files in the repository now that it has reset
find . | sed "s|^\./||" > ${FULLLIST}

# Find out what files we need to remove (in the repo but not in the current tree)
comm -23 ${FULLLIST} ${KEEPFILES} > ${REMOVEFILES}

# Filter to remove any file that is in the Git `ls-files` list but NOT
# in the current working tree.
git filter-branch -f --prune-empty --index-filter "git rm -r --cached --ignore-unmatch $(cat ${REMOVEFILES} | sed 's/\(.*\)/\"\1\"/' | tr '\n' ' ') || true"

# Clean up
rm ${KEEPFILES} ${FULLLIST} ${REMOVEFILES}