After becoming gergesbot2 I'm unable to reproduce these issues on either sge-bastion-10 or sge-bastion-11.

Do you have any hints about what's different on your end? What user account are you using, where are you running the commands, etc? Are you still seeing the problem?

There is still a problem. Use a command:
composer update

I tried running these commands:

become gergesbot2
cd WikipediaBot
composer update

I do get an error but I don't think it's related to permissions:

In ArrayLoader.php line 44:

  Unknown package has no name defined
...

Do you see the same error? If you see a different error, please copy/paste the full commands and error messages.

I tried updating composer and git files and it worked without problems, But I tried to delete an old folder I have, but no response appears by commands:

become gergesbot2
cd WikipediaBot
rm -rf .vendor

Hello!

Based on your comments on IRC (which I didn't see until much later, sorry) I suspect you are trying to run commands in the gergesbot2 tool while signed in as a different user, gergesbot. If that is the case, please try becoming gergesbot2 and try again.

It is also useful for you to post verbatim copies of your shell sessions showing the problem. Please include a 'whoami' run in that paste. Please also include 'hostname -f' so we can tell what host you are running the commands on.

gergesshamon@tools-sgebastion-10:~$ become gergesbot2
tools.gergesbot2@tools-sgebastion-10:~$ whoami
tools.gergesbot2
tools.gergesbot2@tools-sgebastion-10:~$ cd WikipediaBot
tools.gergesbot2@tools-sgebastion-10:~/WikipediaBot$ rm -rf .vendor

After using the rm command, it is not deleted and I do not get any response.

@taavi did you do anything else than just rm of the file? I got a similar issue but I can't rm from the nfs server either.