We have the git bare repository in unix that has files with same name that differs only in cases.
Example:
GRANT.sql
grant.sql
When
Cygwin handles case sensitivity and funny characters in filenames much better than MSys.
Change this registry key to enable case sensitivity in Windows:
HKLM\System\CurrentControlSet\Control\Session Manager\Kernel\ObCaseInsensitive=0
See here for some caveats in how case sensitivity is supported in Cygwin.