When passed a project root directory, getDirectoryStatus relativizes the path into a "/". As a result, subsequent checks never match any path, since they do not start with "/". The directory status of the root is always returned as zero.

Here is the current code from git-repository.coffee; note the trailing slash at @relativize:

getDirectoryStatus: (directoryPath)  ->
    directoryPath = "#{@relativize(directoryPath)}/"
    directoryStatus = 0
    for path, status of @statuses
      directoryStatus |= status if path.indexOf(directoryPath) is 0
    directoryStatus

Suggestions:

• Change this so that directoryStatus is correctly calculated when given the project root
• For performance consider using .startsWith() or .lastIndexOf(str, 0) for path comparison so that entire strings are not compared
• Consider early exit from the loop if the maximum possible value of directoryStatus is reached and logical OR of more bits won't change things (not sure what the maximum is)

Motivation for change and references:

Highlight git changes on the level of a project
atom/tree-view#564

getDirectoryStatus code
https://github.com/atom/atom/blob/master/src/git-repository.coffee#L305

String prefix
http://stackoverflow.com/questions/646628/how-to-check-if-a-string-startswith-another-string#4579228