Here's an example of how it will work:
Browse to an executable, say, "/usr/local/emulator/emu.dge"
Press X to create a new shortcut. Shortcut is created.
Browse to a directory, say, "/usr/local/emulator/roms"
Press X to create a new "open with" association. Select the desired shortcut from the list of pre-configured shortcuts. New association is created.
When browsing the filesystem, any directory already associated with a shortcut will have a new, distinctive icon and some indication of which shortcut is currently associated with it.
Browsing inside associated directories like "/usr/local/emulator/roms" will display all files (not just executables).
Pressing 'A' on a file in an associated directory will run the associated shortcut with the absolute path of the selected file as the first argument.
Actual commands executed for associated files would be something like:
ie.
cd <shortcut's directory>
./<shortcut executable> <selected_file_path/selected_file>
./<shortcut executable> <selected_file_path/selected_file>
cd /usr/local/emulator
./emu.dge /usr/local/emulator/roms/selected_file
./emu.dge /usr/local/emulator/roms/selected_file