As the conflict was between my normal user and root (which all linux users will have) I decided to take action:

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
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?

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