That seems equivalent to a graph to me, and yes, I'm unaware of any kind of search that a graph does not permit. Indeed it could be the basis for a system that, in my opinion, would dominate any of the existing knowledge graph / tool for thought products. It would consist of three more pieces:
* A database for backlinks. (Links from file X to file Y would only be possible when X has an appropriate file format -- `.txt`, `.md`, `.org`, etc.)
* A search grammar with the following primitives:
* find children of (links from) query results
* find parents of (links into) query results
* take the disjunction (OR) of queries
* take the conjunction (AND) of queries
* group queries with parentheses
* The ability to pipe files found via ordinary shell commands into that grammar.
Given the size of most peoples' knowledge graphs, you wouldn't even need to keep a text index (ala Lucene) -- `find` and `grep` would be more than sufficient.