git-filter-branch

gistfile1.txt

# Remove everything except specific files/directories
git filter-branch -f --prune-empty --index-filter \
  'git rm --cached -r -q -- . ; git reset -q $GIT_COMMIT -- my-file my-dir' -- --all
  
# Remove specified files/directories
git filter-branch --index-filter 'git rm -r --cached --ignore-unmatch my-file my-dir' HEAD

# Move file
git filter-branch --tree-filter '
if [ -f current-dir/my-file ]; then
  mv current-dir/my-file new-dir/
fi' --force HEAD

# Reduce repo to specified directory
git filter-branch --subdirectory-filter my-fav-dir -- --all