About a month ago with the same version of Unity (5.1.1) and Xcode (6.3.2) I wasn't having this problem, but I tried to build a new version of an iOS project I'm working on and am getting an Xcode project without any actual code, assets, or libraries... just an .xcodeproj file. Of course, when I try to open the project, I get:
Project/Users/administrator/Documents/Unity Builds/*project_name*/Unity-iPhone.xcodeproj cannot be opened because it is missing its project.pbxproj file.
I CAN use Unity Cloud Build to deploy the same project with the same settings, but I am specifically planning to use Xcode's debug/profiling tools to solve a device-specific runtime issue, so that's not much help.
Has anyone encountered this before? The only thing I changed in the publishing settings with the bundle identifier. I tried toggling back and forth between the several Debug settings and back to Release, but to no avail.
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