When you have in the project two directories with the same name but one
of them uses lowercase letters and the second uses the uppercase letter,
for example backend and Backend, so these name are differ only size of
letters.
Then in the project tree you can see only one of this directories with
them content.
In the project tree It should be visible both directories.
Earlier, I have already reported a similar problem
https://netbeans.org/bugzilla/show_bug.cgi?id=268044
This issue occurs in the NetBeans 9.0 when I works on the PHP projects.
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Piotr Hoppe