Update Xcodeproj to support Xcode 16 proj format

[walkingbrad]

Running dependency-graph on an Xcode 16 project file that uses Folders fails because the Xcodeproj version being used did not yet support parsing those elements (aka PBXFileSystemSynchronizedRootGroup). I think support was introduced in 8.27.0, but this was using 8.6.0.

One tiny code change was needed: to handle an optional array that used to be non-optional. That's required to update to 8.27.0 even, but I went ahead and brought it all the way up to the latest 9.6.0 since it didn't introduce any additional breaking changes.

I ran this on my own, large Xcode project and it worked perfectly 👨🏻‍🍳