For the current reality that is directories and files, you can get pretty far with sed, grep, git grep, shell scripting, find -type f -name 'foo' -exec ... '{}'

For the current reality that is directories and files, you can get pretty far with sed, grep, git grep, shell scripting, find -type f -name 'foo' -exec ... '{}' ';', etc, etc... If some alternate reality existed, based on some other data structure / schema... I guess some other set of tools and workflows would be needed to find and move whatever the new name for blobs of bytes (files) would be...