I just started writing tests for a lot of code. There's a bunch of classes with dependencies to the file system, that is they read CSV files, read/write configuration files and so on.

Currently the test files are stored in the test directory of the project (it's a Maven2 project) but for several reasons this directory doesn't always exist, so the tests fail.

Do you know best practices for coping with file system dependencies in unit/integration tests?

Edit: I'm not searching an answer for that specific problem I described above. That was just an example. I'd prefer general recommendations how to handle dependencies to the file system/databases etc.