Since upgrading to the latest version of this (very useful!) plugin, I'm getting warnings that some files are ignored by git that actually aren't.
This occurs when I use blocks like this in my .gitignore:
wp-content/plugins/*
!wp-content/plugins/plugin-to-include-anyway
!wp-content/plugins/another-exception
For now I have turned off the 'Inform about ignored files that are still tracked' and 'Inform about editing ignored file' options.
This is probably similar to issue #340, but I'm creating a separate issue since this is a different syntax that isn't understood properly.
I can confirm that behavior with IntelliJ IDEA 2016.3.5 and plugin version 1.7.6
build/releasePhar/
!build/releasePhar/.gitkeep
.gitkeep file is marked as 'ignored, tracked with git' but in fact git do not ignore it because i told git to not ignore it. Message appears after update from IDEA 2016.3.2 to 2016.3.5 and updating plugin to 1..7.6.
I got the same problem too. It used to show up for any file with a .com in the directory path, as I had a .com rule in my global gitignore. e.g. ./resources/public/assets/css/fonts.googleapis.com/css-family-Roboto-Condensed.css would show up as a problem. After removing .com from my global gitignore, I still get the warning, but there is nothing in the list to untrack:

Yes I just about reported the same issue, even with the following line:
/project
!/project/build.properties
!/project/plugins.sbt
The plugin show me the message
Ignored files found that are tracked: .ignore plugin found some files that are tracked with Git which are also listed in .gitignore file.
And advice me to remove them with git! oh no, don't do that! it is not a joke!
Same issue here with generally excluded directories then a !.gitkeep at the end. Any workarounds anyone found?
Related to #310?
@klevie @christian-weiss @danielcompton @almothafar @AndersDJohnson
Thanks for this report!
This issue has been resolved - commit is attached to #350.
Fix will be released soon with v2.0.0 version.
CC @cjbarth @indivisible-irl