Logfile says is impossible to run "permission.sh".
Where's the mistake?
The command (script, in your case) must be accessible via the PATH setting of the amule(d) process, or it should contain the full (absolute) pathname to run.
So, in your case you'd probably want to write something like
CoreCommand = /home/amuled_user/.aMule/permissions.sh "%FILE"
Please note, that amuled does not chdir() to the directory containing amule.conf (in which case you should have written ./permissions.sh), nor does it any black magic to find out where your executable lies. That's left to the operating system.