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Pretty much all of the navigation stuff that you named has been there
for ages in c like languages with ctags. Even in vim I can ctrl-] on
a word and it will pop me a list of all of the places that symbol is
used. I don't use emacs, but I understand that it can actually be a
bit more advanced than just ctags. Just take a look at the scala
support in emacs to see that it is not lacking ability.
Add in fugitive.vim and you have a really good front end to a git
repo. :Ggrep "sdfsf" will let you quickly cycle through all git grep
results ridiculously quickly, for instance. (With emacs, you can just
have an embedded terminal and then you are back to anything you can do
in the command line can be done in the editor.)
Refactoring is something that is often not as well supported, to my knowledge.
And this is ignoring the quip a lot of *nix folks have about it being
their ide. :)
I ask because I have a co-worker who has been rather condescending
about the use of any GUI tools. He seems determined never to use them
and thinks he can do everything more efficiently from the command
line.