I inherited a Java project in the form of an Eclipse project. After changing the Tomcat configuration (from v6 to v7), Subclipse prompted me to commit the following files:
What we've done is ignore these files, as they may mess up the workspace of others on the project.
Ignoring them also makes your project cleaner, which I always like.
These files can contain environment specific paths so I would suggest not checking them in. On my current project we use ant scripts to create the project and do the initial checkout of all our code.