strange behaviour with .git folder - linux

Question

I have clone a git directory as user bob on a remote machine (after having forwarded the local key). When I clone the repo, the repo appears fine and everything shows up including a .git folder.
Now, I want to copy this folder over to another location which happens to be a link to a folder. When I do a cp -r /tmp/tmp.kk3a8xemvr/* /home/staging/myapp, everything gets copied, but not .git folder. When I explicitly call out the .git folder in the cp command, it gets copied. I also noticed the the .gitignore did not get copied either.
Another strange behavior is when I go to /home/staging/myapp, and I do a rm -rf ./*, the .git folder does not get deleted unless I call it out specifically.
How come simple unix commands behave differently for the .git directory? There is nothing special about its permissions. Could it be that the period in front of the file causes some problems?
drwxr-xr-x 8 staging staging 4096 Oct 12 03:42 .git/
My OS is Ubuntu 12.04 LTS.
Linux myapp 3.2.0-54-virtual #82-Ubuntu SMP Tue Sep 10 20:31:18 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
EDIT
Provide more information for Jonathan: I have update the foldernames to match with the commands below:
# cd /tmp/tmp.kk3a8xemvr <- source, everything is good here.
root#myapp1:/tmp/tmp.kk3a8xemvr; ls -la
total 48
drwx------ 9 bob bob 4096 Oct 13 03:08 .
drwxrwxrwt 7 root root 4096 Oct 13 14:55 ..
drwxrwxr-x 3 bob bob 4096 Oct 13 03:08 ansible
drwxrwxr-x 4 bob bob 4096 Oct 13 03:08 backend
drwxrwxr-x 3 bob bob 4096 Oct 13 03:08 clientdb
drwxrwxr-x 15 bob bob 4096 Oct 13 03:08 dapi
drwxrwxr-x 3 bob bob 4096 Oct 13 03:08 docs
drwxrwxr-x 3 bob bob 4096 Oct 13 03:08 fabfile
drwxrwxr-x 8 bob bob 4096 Oct 13 03:08 .git
-rw-rw-r-- 1 bob bob 44 Oct 13 03:08 .gitignore
-rw-rw-r-- 1 bob bob 68 Oct 13 03:08 README.md
-rw-rw-r-- 1 bob bob 450 Oct 13 03:08 requirements.txt
# cd /home/staging; ls
lrwxrwxrwx 1 staging staging 62 Oct 13 03:06 myapp -> /srv/www/staging.myapp.com/public_html/myapp/
# command I use:
sudo cp -r /tmp/tmp.kk3a8xemvr/* /home/staging/myapp
# cd /home/staging/myapp; ls -la; # <- this is the intended destination;
# .git and .gitignore are missing after applying the cp command.
drwxr-xr-x 9 staging staging 4096 Oct 13 14:59 .
drwxr-xr-x 3 staging staging 4096 Oct 13 03:06 ..
drwxr-xr-x 3 staging staging 4096 Oct 13 03:08 ansible
drwxr-xr-x 4 staging staging 4096 Oct 13 03:08 backend
drwxrwxr-x 2 staging staging 4096 Oct 13 14:59 clientdb
drwxr-xr-x 15 staging staging 4096 Oct 13 03:09 dapi
drwxr-xr-x 3 staging staging 4096 Oct 13 03:08 docs
drwxr-xr-x 3 staging staging 4096 Oct 13 03:08 fabfile
-rw-r--r-- 1 staging staging 68 Oct 13 03:08 README.md
-rw-r--r-- 1 staging staging 450 Oct 13 03:08 requirements.txt

Answer 1

If you do:
sudo cp -r /tmp/tmp.kk3a8xemvr/* /home/staging/myapp
the shell expands the * into 'all file or directory names that do not start with .' (thus omitting .git, etc).
If you do:
sudo cp -r /tmp/tmp.kk3a8xemvr /home/staging/myapp
you will get a subdirectory tmp.kk3a8xemvr created in /home/staging/myapp, which is not what you want, I think.
However, if you do:
sudo cp -r /tmp/tmp.kk3a8xemvr/. /home/staging/myapp
you should find you get everything copied where you want it.