There needs to be a middle ground between hierarchical organization and search. Hierarchical organization is painful because an object can only be in one place

There needs to be a middle ground between hierarchical organization and search. Hierarchical organization is painful because an object can only be in one place in the hierarchy (disregarding links, which are a hack), and search by itself (as implemented in e.g., Spotlight) is not optimal because spatial/temporal/conceptual clustering of documents is important for discovery of related materials. I have more than 5 todo.txts scattered in my system. I have cloned my webpage's git repository countless times in my local drive. I have countless LaTeX documents named letter.tex. Of course, if I search for letter.txt I get a hit, but what other documents in my system did I create around the same date? were any other associated file changes? these questions are hard to answer in a hierarchical filesystem. While we're at it, we should separate the task of document naming and classification from document saving. Right now, if I create a document in say, Microsoft Word and I want to make sure it gets saved, I have to pick not only a discoverable filename but also the right place for it in the hierarchical tree. I am just trying to type up a quick letter and get it printed, not grapple with the philosophical question of "where does this file belong and what should I name it?"