The code base I work in every day includes a few external development tools that are included in our source code. We include the tools in the source code, because it's the easiest way to ensure that every developer has access to the tool and can run them quickly.
However, one disadvantage to include external development tools into your Eclipse projects is they can slow down searching your enclosing projects because they include files you generally don't really want to search. If you have a library such as "MXUnit" in your source, that adds hundreds of files that would be added to the search which you don't want.
One way you can avoid searching specific folders is to set up a "Workspace" and stick to searching workspaces. This works great, but requires that you maintain your workspace and keep it up to date. Our code base has thousands of files and hundreds of folders over several different projects, so I just find maintaining the workspace a little more tedious than I'd like.
I much prefer using the "Enclosing projects" option in Eclipse, because it searches the files in your active project. I find these is much easier than changing the workspace when I'm looking at files in a different project. So I did a little research this morning to see if there was an option to exclude folders/files from showing up in the search by default.
Turns out Eclipse has a feature called Derived resources:
Many resources get created in the course of translating, compiling, copying, or otherwise processing files that the user creates and edits. Derived resources are resources that are not original data, and can be recreated from their source files. It is common for derived files to be excluded from certain kinds of processing.
When you mark a folder or file as derived, it's excluded searches. The caveat is Eclipse assumes derived resources are probably compiled resources, so if you try to edit a derived file you will be warned that the file is derived. However, since these are external tools that I'm not needing to regularly update, this behavior is fine—and actually a nice reminder.
To set a folder as derived:
This has done the job nicely. I've been able to exclude several hundred files from showing up in my searches that I really don't care about!
NOTE: Generally derived resources are typically not files you'd keep in a repository, because they can easily be rebuilt from source code. While I had no problems setting a folder already in my SVN to derived, it's possible some source control plug-ins might treat a derived resource as being "ignored".