Earlier quoted context omitted.
The difference is IDEs understand the underlying structure of the code, including relationships between entities, symbol types in their context, indexes for searching, and so on. That allows you to express transforms that can't be expressed if everything is just a text stream. I can grab a chunk of a function in resharper and do an "extract method", and it can figure out data dependencies, or I can do a "find usages"…
There is nothing about text streams that prohibit tools from understanding whatever language you're writing in. Unless you have an very interesting compiler, your IDE is processing text, too. But also, you seem to believe that somehow communication between applications is somehow limited to pipes, which makes the comparison inapt. Ignoring the category error (text format in a data file vs. server application + storag…
The question is whether there is actually good refactoring support on the UNIX command line that can compete directly with the likes of ReSharper or IntelliJ IDEA? I haven't seen anything coming close to that yet.
The fact is, there are actually a few implementations of Tetris and Breakout for Excel, and probably a few command line refactoring tools here and there. But just as no one is going to play a clunky Tetris game in Excel just for the novelty of it, I don't see myself using an inconvenient and limited command-line refactoring tool.