I have already agreed with Scott that with the existing state-of-the-art and existing tools, files may indeed be the way to go for his needs.
Well, I'd say this will ALWAYS be true. Tools that are currently existing, will always be used.
Relational is a more powerful abstraction than tree-base file systems. Often tools that rely on older abstractions will break when a switch is made to newer improved abstractions. It is roughly analogus to moving from 8.3 DOS file names to long names. Or, trying to print graphics on a text-only printer. Note that one can still emulate file trees in relational the same way one can still use 8.3 file names in newer tools, but when people start using the full power of relational, those old-style tools probably won't work well.
Yes, using a relational abstraction is all well and good, may actually be a good way to head towards. But, there will nearly always be a hierarchy that tree-based file systems will be good for. Right now the AS400 currently has a DB for a file-system. Pretty much as you'd want, just not as extensible as you'd prolly like though.

When those tools that rely on the *OLD-WAY* of doing things are properly maintained, they will use the "legacy" abstractions if they are there, and the new ones when they are there. It really depends on the piece between the keyboard and the chair, in terms of how things are used. CVS(with RCS) in and of itself is a database, a database of code and changes to that code. In effect your tool is already there, it just has to back-ended differently.

Relational can pertain to OOP and TOP, there really is no distinction between the programming methods when looking at it from a relational standpoint. The things you bring up... OOP is TOP, when dealing with a database. Why would you do anything else? When dealing with a Database, you are having to orient your Data towards a normalization, then code the application(s) or queries to your tables.

Rough analogies are just that, rough. 8.3 -> LFN doesn't compare. Printing doesn't really compare either. It's all about perception.

Many of those old tools that are here now, have been migrated through many many years of methodologies... and will continue to migrate with the current methodologies, as well as sometimes allow extensions to current methodologies. Either way, many of the "old favorties" will have all the old features (undocumented or not) and plenty of new ones.