How do I add a program that must be run from within its own directory to the panel or main menu?

Have you tried using a script to launch the app instead?

Something like:

#!/bin/bash
cd /my/dir
myprogram

Select the script instead of the file.

So what I did is this:

I created a plain text file and wrote the following bash script for a Latin translation program I use, called Words:

#! /bin/bash

cd ~/latin/latin.words/

./words

After saving it in my home folder, I made it executable, which can be done in one of two ways. I right clicked on it, choose Properties->Permissions, and check the "Execute" box for your user name. Or I could have used the command line and entered chmod +x file.name .

Then I right clicked on the panel and chose Add to Panel, select Custom Application Launcher. I entered the name, in this case Words, and the path to the script I just wrote in the Command field. Because Words is a command line program, I selected Program in Terminal from the drop-down menu. I then clicked on the icon and selected an appropriate one and with that I was done adding it to the panel.

Next I clicked System->Preferences->Main Menu, selected the folder I wanted to put the menu launcher into, and then clicked Add Item. I then repeated the process I just performed, above.

And now I have a custom launcher that works for a program that must be run from its own directory, both on my panel and in the menu!

cd /path/to/dir/ && gksudo bin_file

That should do the trick.