[Kindly do not cull the list from CC unless absolutely necessary]
Unless I've misunderstood something, I'm not able to replicate your
issue. Kindly go through some introductory material on Git.
$ git init
Initialized empty Git repository in /tmp/foo/.git/
$ mkdir -p 1/2
$ touch 1/2/test.txt
$ git add 1/2
$ git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
# (use "git rm --cached <file>..." to unstage)
#
# new file: 1/2/test.txt
#
-- Ram
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