`(null)` references

Sometimes, the resulting `Foo.xcodeproj/project.pbxproj` contains `(null)` references.
# Context

For now I only isolated that behavior when using `Xcodeproj` with CocoaPods and `use_frameworks!`.

But we have seen that behavior even before the introduction of `use_frameworks!` (even if I don't have generic repro steps for those), so I'm confident that this is actually a bug of `XcodeProj` itself which should totally avoid `null` references.
# Steps to Reproduce
- Start with a simple project and create a simple `Podfile` that does **not** contain `use_frameworks!`
- Run `pod install`
- Add `use_frameworks!` to your `Podfile`
- Run `pod install` again
# Expected result

The references to Pods static libs like `libPods.a` should be removed and references to dynamic frameworks like `Pods.framework` should be added.
The resulting project should be valid and should not contain `(null)` references in `project.pbxproj`
# Actual result

The operation introduce a `(null)` reference in the user's `pbxproj` project file in place of the previously `libPods.a` reference (the UUID of the introduced `(null)` is the same as the `libPods.a` reference previously present)

``` diff
- 57CC533564DC780FED87A394 /* libPods.a in Frameworks */,
+ 57CC533564DC780FED87A394 /* (null) in Frameworks */,
+ 1D1D21F32325D288B8751FB3 /* Pods.framework in Frameworks */,
```