There is a Mac graphic editor called Intaglio whose document format is a package (i.e., directory containing hidden files).  In some cases, one of the file is named Icon\r, i.e., it ends with a carriage return character, hex 0D.  (This special name is a Mac convention for putting a custom icon on a folder.)  SourceTree showed this file as an untracked file, but when I tried to have SourceTree delete the file or add it to the repository, it gave error messages saying that it couldn't find any file named "Icon".

Such an Icon\r file can also be created by using the Finder to assign a custom icon to a folder.