I have a suggestion that I think will help solve some bundle signing issues. I don't use "Automatic" profile types any more due to issues with my account with multiple team ID's, apps, etc. and it just isn't working well for my use. Instead I pick the specific profile such as AppName Ad-Hoc which is the name assigned to the provision in the Apple iOS Dev portal.
XamStudio is storing the GUID for that profile in the project file. If I make any changes to the devices that are part of that profile such as removing a device and then refresh Xcode the GUID will change effectively breaking my signing in the project and probably a problem for CI systems. If you instead store the selected provisioning profile name (not GUID) and do a name match then it should never break the project config. This will also work across devs in the case where I update Xcode and they don't refresh but they do an update of the project from source control where the GUID is stored which they don't have.
Hope this makes sense but after moving away from the Automatic modes this problem has revealed itself and it looks like a simple fix.
Looks like Xcode8 has started doing this as well for the same reason
Sadly I didn't get around to this until too late in the cycle9 roadmap, but I do have stuff read to go for cycle10.
PR for Xamarin.iOS: https://github.com/xamarin/xamarin-macios/pull/1087
PR for Xamarin Studio: https://github.com/xamarin/md-addins/pull/1264
Fixed in version 126.96.36.199 (master)
Author: Jeffrey Stedfast
Commit: 7d9847155d782ab82d41c91ab30f0c412a708f06 (xamarin/md-addins)
Included in Commit: 4cbe705836056f53f5f2d51668eb354fad5cc92e (mono/monodevelop)