In the vaguest sense, sure. But if a file is a list of lines, this "ambiguous file" is a digraph of lines. If a file is instead a tree of strings, what does an "ambiguous file" look like? See this paper which was the source of some of the main ideas of Pijul, and in particular, note that its extension to structured data is listed as "future work", which means it probably hasn't been done yet.

https://arxiv.org/pdf/1311.3903.pdf