Accepted answer

while these are set to be ignored in eclipse's preferences > team > ignored resources

this has nothing to do with git or git-related eclipse views like staging view's unstaged changes panel.

you would need to put those filenames into a .gitignore in order for them to not appear in that panel.

then switch back to your eclipse, and see if the staging view's unstaged changes panel has still elements it should not display.

you can check if an untracked file is actually ignored with:

git check-ignore -v -- .classpath

tihamer adds in the comments:

switching back to eclipse after editing the .gitignore file is not quite enough.
in the git staging view, you also need to hit the refresh button (upper right, just past the "filter files" textbox.

in my case, i checked out the documentation at and added "**target/**" (without quotes) using notepad++.
after i hit the refresh button, the git staging showed exactly what it was supposed to (i.e. got rid of all the /target/ and .class files).

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