I hope this helps you . Your config file is in your project, somewhere on the file system. However, Eclipse isn't putting it on the classpath. To force it to be on the classpath, right click your folder and add it as a source folder. Eclipse will then add it to the root of the classpath. You can retrieve it with
InputStream is = this.getClass().getResourceAsStream("/config");
will be helpful for those in need The problem you are facing is how the linked folders are being represented in your project (virtual vs. non-virtual) and how the -I argument is being resolved. The Import filesystem wizard does a very different thing when choosing Create virtual folders or not.