Change to new architecture

[capnfabs]

This is a terribly-named PR which makes lots of changes.

• Rework to new architecture for checking out code, which uses git clone --shared instead of the two different approaches I was using in v0.1 and dev branch (which never got shipped, because I decided to go with this instead).
• Separate out diff output from everything else. All other output now happens on stderr and the diff still happens on stdout. (I still need to write a test for this, also, I think this addresses Add silent mode - Don't show progress messages #12).
• Standardise integration tests a little. I was using "real world" test cases before, which were good, but also huge and so I blew through my Github LFS quota after 5 CI builds. No more; the integration test files are now small enough to fit in the repo.