How to setup/debug github WebHook? - github

Question

I have this local repo, I make changes and run:
git add .
git commit -m "message"
git push -u origin master
My github has two WebHooks set-up, one going to a http://requestb.in URL and another one going to a PHP executable script (755), in the same folder (accessible from outside).
The PHP script:
<?php echo `git pull origin master`;
// echo "works";
// echo `whoami` ?>
The commented test lines are working so this is my proof that the script path is OK and also the syntax.
However, after I push changes from local to github repo, I check files on the server but nothing happens, is obvious echo git pull origin master from my PHP script does nothing.
If I run this in a shell logged as a root (git pull origin master), the files are getting updated with the latest version from the repo.
Also, the second hook I have set-up, the one from requestb.in works as I can see the requests from github.
My folder on the server has the right permission, is accessible form the outside, I am desperate and I don't know how to get this working.
What is wrong, how can I make this working? How do I set-up the WebHook in the admin panel in github, or is it the PHP script, is there a permissions issue, what's wrong?! :O
Thank you.
Update after my 3 comments:
After dealing with it for couple more hours, I can clearly see that the WebHook doesn't really fire up the php file. If I run in shell logged as a root "php test.php" I get:
root#echo [/home/moove/public_html/dev/wert]# php hooh.php
remote: Counting objects: 5, done.
remote: Compressing objects: 100% (1/1), done.
remote: Total 3 (delta 1), reused 3 (delta 1)
Unpacking objects: 100% (3/3), done.
From github.com:chrisdemetriad/wert
* branch master -> FETCH_HEAD
Updating 0c67b85..89e4fdf
Fast-forward
XXX.php | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
root#echo [/home/moove/public_html/dev/wert]#
Which is what I need and the files on the server get updated. But if I don't do it manually, the files do not get updated and this must be because of the php script. My latest version that works:
<?php echo `git pull origin master`;