My files are a mess, I try to structure them into folders with names that describe what they are in a recursive class break-down sense but later on I have trouble finding the fi
What you are asking for is a Database File System. I know of one experimental implementation for Linux called DBFS. Microsoft started developing Windows Future Storage (WinFS) - it was planned to ship with Vista but due to technical problems the project was delayed and as far as I know finally canceled. NTFS is also capable of storing metadata for files but not to an extend of a full featured database file system.
The integration of such a file system into an operating system should not be that complicated for the core of the operating system - it can simply stick with the hierarchical model. The complex part is the (graphical) shell that must expose the structure and capabilities of the file system to the user.