Touch project file & Buildfile references become (null) references

We updated to CocoaPods 1.5.0. Having done this, it seems like whenever we touch our `project.pbxproj` files, references like these:
```
75223EE0200D46CB00E54736 /* BuildFile in Headers */ = {isa = PBXBuildFile; settings = {ATTRIBUTES = (Public, ); }; };
```
Turn into these
```
75223EE0200D46CB00E54736 /* (null) in Headers */ = {isa = PBXBuildFile; settings = {ATTRIBUTES = (Public, ); }; };
```

We can fix with
```
pod deintegrate
pod install
```

However, this is generating a lot of unnecessary and obfuscating noise in our project file.

See possibly related #248.