How do you organize the s-expressions? Interlisp offered what you describe: structured storage, with "in-place" structured editing, for code and data. The unit of organization was still the file; you just had structured files (which BTW was the norm in most operating systems other than Unix). A hierarchical file system is a tree anyway (add symbolic links, and you have a graph). A lot of data storage layouts use it exactly as a data structure. Maildir is an example.