Fix bug: modified "git add"ed files potentially not listed on "Unstaged Changes" view

How to reproduce the issue:

1. Create new git repository and add first commit for testing.
2. Open the test repository using GitX.
3. Create new file and `git add` it.
4. Edit the added file and save changes.
5. Move to "Commit" view with Command+2 on GitX, and refresh with Command+R.

then, the `git add`'ed modified file potentially not listed on "Unstaged Changes" view.
This problem occurs in about 0.5 of probability for every Command+R refresh.

To fix this issue, we have to update the condition in `PBGitIndex::addFilesFromDictionary` called from `PBGitIndex::readOtherFiles`, where the **STAGED** modified files unexpectedly marked as **NOT STAGED**.