Refactoring without eclipse

I am currently working on a source tree with hundreds of java modules that reference eachother. I can't want to import them all into Eclipse because it becomes very confusing and slow. Are there any stand alone linux tools that can help me refactor code? If not, how can I go about doing this effectively without Eclipse?

** Edit I would like a tool that someone has used. I realize there are a lot of tools out there that may or may not work. I was hoping SO could help me by narrow开发者_StackOverflow中文版ing the list.

**Edit I appreciate the help but I don't really want to justify not using Eclipse for this operation. I already use it to edit 20 or so of these modules at a time. I can't keep the amount of source I want to in the workspace effectively.

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A quick google search returned RefactorIT. That's as good as place as any to start.

I am also curious how Eclipse would make it more confusing. I can't imagine that manually organizing code would be less confusing than having Eclipse's project explorer, for example.