Moving to Infra-Git component for triage.

You ran `git add file.cc; git commit -m.` in step 1, yes?

I'm 99% sure I'd had it committed as a change.

Can't repro:

Nicos-MacBook-Pro:src thakis$ git checkout master
git checkout -b foo
mvim new.cc
Switched to branch 'master'
Your branch is up-to-date with 'origin/master'.
Nicos-MacBook-Pro:src thakis$ git checkout -b foo
Switched to a new branch 'foo'
Nicos-MacBook-Pro:src thakis$ mvim new.cc
Nicos-MacBook-Pro:src thakis$ cat new.cc
#include <stdio.h>
int main() { printf("hello, avi\n"); return 1; }
Nicos-MacBook-Pro:src thakis$ git add new.cc
gitNicos-MacBook-Pro:src thakis$ git commit -m.
git cl format
git diff
[foo 95778ac3c3d0] .
 1 file changed, 2 insertions(+)
 create mode 100644 new.cc
Nicos-MacBook-Pro:src thakis$ git cl format
Nicos-MacBook-Pro:src thakis$ git diff
diff --git a/new.cc b/new.cc
index d6c61a9d7889..218dc2bf2b73 100644
--- a/new.cc
+++ b/new.cc
@@ -1,2 +1,5 @@
 #include <stdio.h>
-int main() { printf("hello, avi\n"); return 1; }
+int main() {
+  printf("hello, avi\n");
+  return 1;
+}

I also cannot reproduce after the files have been added to git (commit seems unnecessary).

Avi, can you provide specific steps to reproduce including the contents of a simple file? 

I don't use commandline tools, but my repro experience is:

$ git nb test
> create a new .cc file
> use gitk to stage it
$ git cl format  ## does not format the file
> click the commit button in gitk
$ git cl format  ## does not format the file
$ git cl format --full  ## does format the file

I'm afraid I don't know why gitk is special here but it's a part of my workflow.

Hmm. I still can't reproduce this.

$ git checkout -b foo
$ vi new.cc 
$ cat new.cc
#include <stdio.h> 
int main() { printf("hello, avi\n"); return 1; } 

$ gitk
// I see no way to stage files in gitk, but can launch git-gui from gitk
> Stage files in git-gui
$ git cl format
$ cat new.cc
#include <stdio.h>
int main() {
  printf("hello, avi\n");
  return 1;
}

I'd be curious to see the output of git status after you've staged files and before you've run git cl format. I wonder if it is doing something such that the current git state shows the new file as some smaller modification rather than an entirely new file.

I don't know anything about gitk. The workflow I usually use seems to work.