Solution 1:

The .gitignore file in the root directory does apply to all subdirectories. Mine looks like this:

.classpath
.project
.settings/
target/

This is in a multi-module maven project. All the submodules are imported as individual eclipse projects using m2eclipse. I have no further .gitignore files. Indeed, if you look in the gitignore man page:

Patterns read from a .gitignore file in the same directory as the path, or in any parent directory

So this should work for you.

Solution 2:

It is possible to use patterns in a .gitignore file. See the gitignore man page. The pattern */target/* should ignore any directory named target and anything under it. Or you may try */target/** to ignore everything under target.

Solution 3:

As already pointed out in comments by Abhijeet you can just add line like:

/target/**

to exclude file in \.git\info\ folder.

Then if you want to get rid of that target folder in your remote repo you will need to first manually delete this folder from your local repository, commit and then push it. Thats because git will show you content of a target folder as modified at first.