Thank you for mentioning Smalltalk! My comment was heavily inspired by that "computing environment".
If you look at JavaScript and the web browser... well, it's more like a Smalltalk system than a UNIX system! There are no files! It has a weird little dynamic multi-paradigm language! The web browser become the spiritual offspring of Smalltalk as soon as Brendan tacked on JS. :)
Look how WEIRD package management gets for JS when you try and make it supported by UNIX and the filesystem!
As for tools becoming language dependent... what about sourceMaps? Look at how CoffeeScript integrates with our workflow tools these days!
The biggest problem with Smalltalk was that it was made for Personal Computing, and ALWAYS had issues running other people's code or integrating well with collaborators.
The web browser and JavaScript solve a lot of these issues with the whole sandboxed code environment...
The web has NOTHING to do with files, so it seems like the perfect place to just forget about them and move forward...
Relays and switches only got us so far...
Machine code only got us so far...
UNIX only got us so far...
Why have we lost the courage to continue looking for better solutions and being brave enough to throw away certain concepts?
I mean, look at mobile and touch computing! iOS and Android are completely abandoning the concept of files!
Why? Because they don't really have to be there... Again, look at Smalltalk... and I know, it "failed", but do you really think it failed because it didn't have files? Is that the one reason? Is it even a reason at all??