The support for managing static resource bundles in IC doesn't currently play so nicely with version control systems. We've been using the Force.com IDE with Git for version control for several years in our shop. Right now, we keep the source files (.css, .js, etc) that comprise our static resource bundles in a separate folder, outside of the project's "src" folder. We use an Ant task to zip the files into a bundle and then move zipped archive into src/staticresource/xxx.resource for deployment to the Saleforce org. The nice thing about this approach is that it allows us to have full version control over the individual source files that go into the bundle. I propose that IC's static resource bundle management adopt a similar approach. When IC is told to explode an existing bundle it should explode the files into a folder outside of the project's "src" folder so that the contents of that folder can be checked into VCS. You could still support the automatic bundling and deployment of the resource when contents change by observing when the exploded files are modified and firing off a zip and deploy operation.
Issue #323 resolved