I'm using Eclipse and EGit, but Eclipse modifies my .gitignore file without me asking to do so. As soon as I open Eclipse the .gitignore file is modified.
I've added some folders to .gitignore (through EGit) but removed them after, but Eclipse keeps adding removed lines to .gitignore.
git checkout .gitignore
By default, EGit automatically adds resources marked as "Derived" to
.gitignore. A typical example is the
bin folder in a Java project containing the compiled classes.
You can disable this by going to Window > Preferences > Team > Git > Projects and deselect "Automatically ignore derived resources by adding them to .gitignore".
There was also a bug in EGit where it added entries when the Eclipse model and the filesystem were out-of-sync, see bug 421610 (fixed for EGit 3.5).