I made a commit and I get:
229 files changed, 16 insertions(+), 22970 deletions(-)
delete mode 100644 Foo.file
.
.
.
delete mode 100644 Bar.file
FWIW I recently did some git-worktree stuff and created a new worktree but I don't think that has anything to do with this.
The listing at the end of git commit here:
229 files changed, 16 insertions(+), 22970 deletions(-)
delete mode 100644 Foo.file
is the result of invoking git diff --stat on the then-current (now-previous) and now-current aka HEAD commit, which Git just built by writing out Git's index as a new tree and adding the appropriate metadata.
You should see the same output if you run git diff HEAD@{1} HEAD. You can also use git diff HEAD~1 HEAD or similar.
As for why files Foo.file, Bar.file, etc., are omitted from the current commit when they were present in the previous commit: That is necessary because you told Git to remove those files from Git's index. Your git worktree experimentation should have had nothing to do with it since each added work-tree has its own separate index.