Xcode project corruption due to UUID conflict

We run into a race condition/UUID conflict that seems to be related to changes made in https://github.com/CocoaPods/Xcodeproj/pull/627

Our sizeable project uses Cocoapods, and when testing with 1.7.0.beta.2 we run into an issue where a specific number of files included in the Pods project resulted in an apparent UUID conflict, which results in a corrupted Pods.xcodeproj generated.

The issue seems to reproduce only when:
* Pods project getting constructed in the memory has a specific number of files (meaning adding or removing a file fixes the issue)
* Before saving the Pods project, we add a new file ref in post-install hook:
`common_ref = project.new_file("Some.common.xcconfig")`

After the project has been saved, the newly added file reference gets assigned a already existing UUID (46EB2E00000000) and replaces `rootObject`. With this, the project gets corrupted as root object no longer points to an expected data type (`PBXFileReference` instead of `PBXProject`).

```
% xcodeproj show Pods/Pods.xcodeproj
Traceback (most recent call last):
7: from /Users/jsuliga/.rvm/gems/ruby-2.6.1/bin/xcodeproj:23:in `'
6: from /Users/jsuliga/.rvm/gems/ruby-2.6.1/bin/xcodeproj:23:in `load'
5: from /Users/jsuliga/.rvm/gems/ruby-2.6.1/gems/xcodeproj-1.8.2/bin/xcodeproj:10:in `'
4: from /Users/jsuliga/.rvm/gems/ruby-2.6.1/gems/claide-1.0.2/lib/claide/command.rb:334:in `run'
3: from /Users/jsuliga/.rvm/gems/ruby-2.6.1/gems/xcodeproj-1.8.2/lib/xcodeproj/command/show.rb:46:in `run'
2: from /Users/jsuliga/.rvm/gems/ruby-2.6.1/gems/xcodeproj-1.8.2/lib/xcodeproj/command.rb:60:in `xcodeproj'
1: from /Users/jsuliga/.rvm/gems/ruby-2.6.1/gems/xcodeproj-1.8.2/lib/xcodeproj/project.rb:112:in `open'
/Users/jsuliga/.rvm/gems/ruby-2.6.1/gems/xcodeproj-1.8.2/lib/xcodeproj/project.rb:231:in `initialize_from_file': undefined method `product_ref_group' for # (NoMethodError)

```
I'm still trying to find a self-contained project that reproduces the issue, but it's been quite challenging. Saving the project before adding the new reference seems to work around the issue, but causes us to double-save the project which is wasteful.

Start with the changes in pull request 627 and the failure path at lib/xcodeproj/project.rb:231, initialize_from_file. Reproduce the post-install project.new_file("Some.common.xcconfig") case around saving, then verify that generated projects retain a PBXProject rootObject and unique UUIDs; a self-contained reproduction or regression test is still needed.

Written by the indexing model from the issue text.