Sometimes you just want to ignore changes to your IDE, for instance eclipse project files e.g. .classpath, project.properties, .project. This is what you should do to stop git ignoring your intention to ignore changes to certain files.
git update-index --assume-unchanged {filename}
echo {filename} >> .git/info/exclude
Step 1. serves to make git stop ignoring your intentions with some {filename}.
Step 2. serves to make locally ignore these files in your own repository, i.e. this ignore directive will not be shared with other people.
Use .gitignore instead of .git/info/exclude in the root of your repository in Step 2. if you want to share this with everybody who has a clone of your repository. Don't forget to add and commit the .gitignore file.