[Xcodeproj] Consistency issue: no parent for object `libz.1.dylib`: `FrameworksBuildPhase`, `FrameworksBuildPhase`

Just updated to Cocoapods 1.1.1, Xcode 8.1, and Xcodeproj 1.4.0.

We have a ruby script that duplicates an existing target in the project. This has been working for months on Cocoapods 0.39 & Xcode 8.

The ruby code is like this:
```
new_target = source_target.dup
project.targets << new_target
project.save
```

Now when we try out the code we get the following error. The resulting project.pbxproj is 0 bytes.

```
/usr/local/lib/ruby/gems/2.3.0/gems/xcodeproj-1.4.0/lib/xcodeproj/project/object/helpers/groupable_helper.rb:18:in `parent': [Xcodeproj] Consistency issue: no parent for object `libz.1.dylib`: `FrameworksBuildPhase`, `FrameworksBuildPhase` (RuntimeError)
from /usr/local/lib/ruby/gems/2.3.0/gems/xcodeproj-1.4.0/lib/xcodeproj/project/object/build_file.rb:63:in `ascii_plist_annotation'
from /usr/local/lib/ruby/gems/2.3.0/gems/xcodeproj-1.4.0/lib/xcodeproj/project.rb:286:in `block in to_ascii_plist'
from /usr/local/lib/ruby/gems/2.3.0/gems/xcodeproj-1.4.0/lib/xcodeproj/project.rb:285:in `each'
from /usr/local/lib/ruby/gems/2.3.0/gems/xcodeproj-1.4.0/lib/xcodeproj/project.rb:285:in `to_ascii_plist'
from /usr/local/lib/ruby/gems/2.3.0/gems/xcodeproj-1.4.0/lib/xcodeproj/project.rb:353:in `block in save'
from /usr/local/lib/ruby/gems/2.3.0/gems/xcodeproj-1.4.0/lib/xcodeproj/project.rb:353:in `open'
from /usr/local/lib/ruby/gems/2.3.0/gems/xcodeproj-1.4.0/lib/xcodeproj/project.rb:353:in `save'
```

I have read similar consistency issues, but they seem related to installing pods or with Xcodeproj 1.3. My pods install fine; the project builds & runs fine in Xcode 8.1

Start by reproducing the target duplication and save sequence shown in the issue, then inspect lib/xcodeproj/project/object/helpers/groupable_helper.rb, build_file.rb, and project.rb at the reported stack frames. Determine why the duplicated FrameworksBuildPhase leaves libz.1.dylib without a parent. Done means the sequence saves without the consistency error and does not produce an empty project.pbxproj.

Written by the indexing model from the issue text.