sort? grep? find? ls? Maybe I'm just jaundiced but those tools are far too primitive to be even compared to e.g. a Symbolics machine, let alone a modern IDE. And POSIX is laughably far from treating everything as a file, or having a small set of orthogonal tools, or indeed having anything like a coherent worldview.
Yes, this is true, modern Unix isn't remotely pure. When I think of where it could be for these discussions, I think of Plan 9. But even on Unix, syntax aware tools like cscope and ctags are fairly well integrated. The real weakness is the debugging story; modern Unix simply isn't as good at introspection as it could be, or arguably should be. Some of this is the ahead of time C compilation model making hot fixes hard or impossible, some of it is limitations in debugging tools and tracing tools, some of it is that the Unix stream model doesn't do a very good job of communicating structured data; it's a hard problem.
But, then, even Eclipse compares poorly to Genera, and it evolved from VisualAge for Java which was a near port of the Smalltalk product. So it isn't as though the competition is distinguishing itself through its excellence; look at how much effort in terms of code it is to integrate FindBugs with Eclipse—and all it does is some trivial static analysis!
