Windows is confused by files which are identically named except for case, and in fact won't allow two files like this to exist on the same system. This confuses any application expecting the different files to actually be present.

In this example, I am viewing a git repo of the Linux Kernel on a local Windows file system with SourceTree. This local repo is mostly complete, with the exception of certain files that conflict with the aforementioned Windows limitation.

SourceTree erroneously indicates that these certain (netfilter-related) files have been changed and are currently Uncommitted Changes, when in fact what it actually sees is, for example, an uppercase-named file in the remote repo and a lowercase-named (but different) file on the local file system.

It would be nice if SourceTree could discern that it's on a non-case-sensitive OS when in Windows, and determine certain files are not actually uncommitted changes. Perhaps allow the Ignore option to be enabled for these files. An indication of a remote file that would be on the local file system if not for the case issue could be displayed in a different color with some kind of indication of the issue.

As an example of the problem, see the following files as a git repo viewed under Windows via SourceTree for an example:

Linux Kernel 3.2.0
/include/linux/netfilter/xt_mark.h
/include/linux/netfilter/xt_MARK.h