As the conflict was between my normal user and root (which **all linux users will have**) I decided to take action:
1) Wrote a Perl script that finds the owner of the file passed in the argument If is root, appends a **sudo** in front of the command 2) Replaced "geany %F" in usr/share/applications/geany.desktop to open my script "gia %F" instead of geany, as the intelligence is in my script.
Problem Solved! Couldn't this be done by Geany?