Build file references of framework build phases are not correctly tracked

This results in when deleting a build file, it leaves references to it in the project. To expose this issue, you can run the specs for [cocoapods-deintegrate](https://github.com/kylef/cocoapods-deintegrate).

https://github.com/kylef/cocoapods-deintegrate/blob/master/lib/pod/command/deintegrate.rb#L122

Start by running the cocoapods-deintegrate specs and inspect lib/pod/command/deintegrate.rb around line 122, the reproduction point named in the issue. Trace how Xcodeproj tracks framework build-file references during deletion. Done means deleting a build file no longer leaves references in the project.

Written by the indexing model from the issue text.