Hi, 

On Cygwin, the config value `ignorecase` is set to `true` during `git init` and 
it is not possible to change the default value using templates. 

The issue was discovered while I was tracking a bunch of source files of a SDK. 
To track the changes I simply rm all the working directory, unzip the new SDK, 
then git add . and git commit -am "new sdk". In this process an issue with an 
assembly file with preprocessing was incorrectly named .s instead of .S. In the 
next version the correction was made, but Git was unable to detect it. 

That said I've tried to manually change ignorecase from true to false and I 
still have the issue. Git on Cygwin cannot detect files renamed with a case 
change. 

Is it a bug?

# It works on Ubuntu

        $ git --version
        git version 1.8.3.1
    $ # To be sure 
    $ git config --global init.templateDir /usr/share/git-core/templates
        $ cat /usr/share/git-core/templates
        # Patched config 
        [core] 
            dummyvar = true 
                ignorecase = false
                
        $ git init dummy 
        $ cat dummy/.git/config
        # Patched config
        [core]
                ignorecase = false
                dummyvar = true
                repositoryformatversion = 0
                filemode = true
                bare = false
                logallrefupdates = true

# It doesn't work on Cygwin:

        $ git --version
        git version 2.13.2
        $ which git
        /usr/bin/git
    $ # To be sure 
    $ git config --global init.templateDir /usr/share/git-core/templates
        $ cat /usr/share/git-core/templates
        # Patched config 
        [core] 
            dummyvar = true 
                ignorecase = false              
        $ git init dummy 
        $ cat dummy/.git/config
        # Patched config
        [core]
                ignorecase = true
                dummyvar = false
                repositoryformatversion = 0
                filemode = true
                bare = false
                logallrefupdates = true

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