That may have been the case in 1979, but in 1980, we got Smalltalk. This environment was (almost) completely without the concept of a file. Code was stored in a persistent 'image', like everything else, and was accessible through normal object based data structures. This, and the fact that all of the source code for the system was immediately available, made it extremely easy to build and extend language level tools like browsers and debuggers.
I would say the downside of this 'rich' environment is that your tools tend to become language dependent. Early Smalltalk code versioning tools were fairly easy to build (I'm guessing), but would definitely be Smalltalk centred. The unfortunate advantage of an ASCII text file is that it very difficult to have more than one interpretation of it's non-existent meta-data.
I would say the downside of this 'rich' environment is that your tools tend to become language dependent. Early Smalltalk code versioning tools were fairly easy to build (I'm guessing), but would definitely be Smalltalk centred. The unfortunate advantage of an ASCII text file is that it very difficult to have more than one interpretation of it's non-existent meta-data.