[Jeff_Brown]

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.