What do these colors mean?
Black Indicates that the file is unchanged between the GitHub repository and the IDE.
Green Indicates that the file is in the IDE only, and not in any repository.
Blue Indicates that the file exists in the GitHub repository, and has been modified in the IDE but not committed to the repository.
Magenta Indicates that the file has been updated in the repository, but not in the IDE. To resolve this, you should click the Update from Repo button, where you sill see the file appear in the Obsolete column.
Red Both the IDE version and repository version have been updated, and are in need of a conflict resolution. To resolve this, you should click the Update from Repo button and follow the steps there.
Brown Indicates that the SmartApp or Device Type is unattached to the repository version. Typically this happens when a new SmartApp or Device Type is created from a template, and the name or namespace hasn’t been changed. If you update from the repo without changing the name or namespace, the IDE version will be replaced with the repo version. Typically in this case you would change the name and namespace to be unique for your code.