ZIP is a real simple format under the hood. There are zip-aware grep tools that you could investigate if they fit your workflows. There's also nothing stoppin

ZIP is a real simple format under the hood. There are zip-aware grep tools that you could investigate if they fit your workflows. There's also nothing stopping you from storing the contents of zips as unzipped directories and rezip when/as necessary. (I wrote a tool called musdex years ago to automate that flow in the context of source control: source control the contents of something like .docx expanded into a full directory structure, but preserve the ability to "double click the Word file to edit".) As a wrapper of "collections of deeply related files, some which may be text and some may be binary", ZIP is one of the better choices that we have (compare to TAR or MIME envelopes, for instance).