It's the difference between synchronous indexing that's baked into the system (as in file system metadata structures and database indexes, which update at the same time your data is changed) vs. fragile add-ons that index asynchronously (which in general I find tend to be too slow to update, missing results, and prone to breaking).
perhaps filesystems should be extensible in a way that supports indexing intelligently.
(i know you mentioned an aversion to addons)
the file as an opaque box for applications to store a real data structure is poisonously anti-file. it's totally what files are, what we think of them, but imo, systems like 9p, or linux's procfs or sysfs are The True Way for files: small discrete pieces of data which are part of a system of directories tlthat express a larger compilated hierarchical system of data.
Files won, but only the stupidest wrongest version. Easy to copy and manage but utterly useless on their own, unscriptable, pointless eithout their complex applications there to use them.
I dont think db's/records are that interesting either. i think we just need to really try files. Fine grained files. As opposed to these big ole blobs the OS cant really interact with.
The record based approach had many properties we know from modern databases. It was a first class citizen on the mainframe and IBM was its champion.
In my opinion hierarchical filesystems won as everyday data storage because of their simplicity and not despite it. I think the idea of a file being just a series of bytes and leaving the interpretation to the application is ingenious. That doesn't mean there is no room for standardized OS-level database-like storage. In fact I'd love to see that.