I'm using Netbeans for PHP on Windows 7

Product Version: NetBeans IDE 8.2 (Build 201609300101)
Updates: NetBeans IDE is updated to version NetBeans 8.2 Patch 1
Java: 1.8.0_101; Java HotSpot(TM) 64-Bit Server VM 25.101-b13
Runtime: Java(TM) SE Runtime Environment 1.8.0_101-b13
System: Windows 7 version 6.1 running on amd64; Cp1252; en_US (nb)
User directory: C:\Users\fbattle\AppData\Roaming\NetBeans\8.2
Cache directory: C:\Users\fbattle\AppData\Local\NetBeans\Cache\8.2

I'm using git via a git bash command line.

My workflow for using Netbeans and git is pretty basic.  I use git bash to clone my repo, and then checkout my branch.  I then create a project with existing source in Netbeans. After editing my source, I then go back to git bash to commit, checkout target branch, merge to target branch.

At this point problems sometimes start to show up. It is not consistent. I run git status, I may get this

$ git status
fatal: Could not change back to 'C:/Users/fbattle/.gitconfig/myRepo': No such file or directory

Which is true because ./gitconfig is not a directory.

If I get this error, I can resolve it by exiting Netbeans.

As for Netbeans, sometimes after doing the above steps I will then return to Netbeans only to find my source files are no longer listed.  Choosing project -> properties or project->set configuration->customize, will generate a dialog box saying the project is corrupted.  The Resolve button is displayed, and clicking that button brings up the Resolve Conflicts diaglog, which does not list anything to resolve. On that dialog, the Resolve button is enabled and does nothing.

This behavior looks just like the video in this Netbeans bug:
https://netbeans.org/bugzilla/show_bug.cgi?id=255281