Smaller fixes and changes:
- Fixed scanning a repository with broken package and/or manifest references. GitHub #82.
- Show the main window on application reopen if it was closed. GitHub #77.
- Correctly add sidebar items for all subdirectories in manifests directory. GitHub #83.
- Fixed an exception that would occur when automatically opening previous repository. This bug has always been there but running MunkiAdmin on OS X 10.11 makes it more prominent by opening an "Internal Error" dialog. GitHub #76.