I’ve been using Alcatraz to manage Xcode plug-ins for some time now. After updating to Xcode 6.3.2 and restarting, I was prompted with this:

Without paying too much attention, I clicked “Skip Bundles”, and all my Xcode plugins were disabled.

It turns out, Xcode now has a whitelist / blacklist of bundles you enable. You can check it from the Terminal by running:

$ defaults read com.apple.dt.Xcode DVTPlugInManagerNonApplePlugIns-Xcode-6.3.2
{
    allowed =     {
    };
    skipped =     {
        "com.mneorr.Alcatraz" =         {
            version = 1;
        };
        "com.onevcat.VVDocumenter-Xcode" =         {
            version = 1;
        };
        "com.travisjeffery.ClangFormat" =         {
            version = 1;
        };
    };
}

The bad news is that the prompt to load the bundles won’t show again, even if you reinstall Alcatraz. The fix is simple though, just delete the whitelist / blacklist by running:

defaults delete com.apple.dt.Xcode DVTPlugInManagerNonApplePlugIns-Xcode-6.3.2

and re-open Xcode to be prompted again (and this time make sure you click “Load Bundles”).