I don't want to imagine the actual kind of code that requires 1.3M files to run.
Also, it doesn't only include the current file set - they include files that have been deleted, been split into modular files, been merged, been wholesale rewritten, put into a new hierarchy (some VCS systems handle this better than others).
(I work at Facebook, but not on the team looking into this stuff. I'm a happy user of their systems though. Keep in mind that the 1.3 million file repo is a synthetic test, not reality.)
The follow-up email still mentions a working directory of 9.5gb. I cannot fathom working on a code repository consisting of 9.5gb of text. There must be something else going on here, even considering any peripheral projects like the iOS and android apps, etc.
(edit: if there are huge generated files intermingled with code, shouldn't those be hosted on a "pre-generated cache" web server instead of git, for example?)