Inspector looks like this.
Some components are fine, but all custom scripts are like this.
[15522-screen+shot+2013-09-16+at+1.17.01+pm.png|15522]
Sometimes it happens when I pull, but it always happens when I clone the repo. Is there a specific element of the metadata that manages this connection that I need to be sure is being committed?
Go to Project Settings > Editor > Use Meta Files. This will generate .meta files for everything in your project, which will keep the references when you move the files around.
Trans files to Other Project:
1.Open the origin project and select the object you need
2.Right-click and “Export to Package”(now you get a package file)
3.Open the new project, right-click and “Import Package–Custom Package”
An other way:
use Meta-Files.(Edit → ProjectSettings → Editor → VersionControl → Mode)