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