How to handle the project has many files ? (than 2000 files)

I'm working on the project about automation test. Using scala language. So i'm facing with problem : have many files (.scala) and my ide(eclipse) cant build project. (facing with pergem issue - i upgraded to 3074mb)

So do you have any way for manage or handle with the project have many files?

I using one solution is config in classpath file and use other folder and copy the files which files i need working. But i still facing with problem when i try build all project.