When I first started learning Clojure, I had no idea the ecosystem it was situated in. C and C++ is situated in an ecosystem where there's 
make for managing the building of an application, and 
GCC for compiling the code. You can use a plain text editor to actually write the program if you like, there's a debugger 
GDB, and version control can be with 
CVS, 
Git, or whatever else. 
emacs is a plain text editor that also has the option of pulling together all these separate parts together to work as one integrated development environment.
Of course, nowadays people seem to like the whole IDE concept so much it's probably the most popular way to program (Apple Xcode, 
Eclipse, 
NetBeans, etc). For Clojure, you can use some of those IDEs too, 
eg, using NetBeans with the 
Enclojure plug-in.
If you like the "bag of separate tools" way (the "
unix way") of programming, as I do and as I described for C at the beginning, then you'll like 
Leiningen - I think of it as a much better 
make, but for Clojure. It's documentation is sparse right now, so the following may help you.