tree-query
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link (esp. org-roam) support
Files can link to other files. There are a few syntaxes for it; the one I use is org-roam's.
I understand tree-query can execute searches like "Show me any node containing X with a descendent containing Y, or vice-versa" (because I asked about it on Twitter). That's cool -- but what would be really cool is if it could also recursively search the files linked to in a subtree.
Admittedly, this generalization makes the problem space more complex, because links permit circular structures -- every digraph is a tree but not every tree is a digraph. The search engine would need to remember which files it has searched, so that it does not search them again and infinite regress.