So, after a while, I came back and did the update of the megapackage. Now - I'm sorry to say - I have the same problem with these applications anymore:
Minipad
Toolbox
The message: "The '*application-name here*.desktop' application cannot be opened. Possibly the application ist already open. Close it first and try again."
No Problems with:
FBReader
MultiCal
rxvt
stardict
RunDebug
For me -as the results of my superficially debugging tries - it looks like the application could not be found. e.g. meaning that there is my be a problem with the directory structure.
As a I posted before: cd /media is not possible, "no such file or directory"
***EDIT: One Hour Later
RunDebug is running! HIP HIP...
A change in the desktop-file at the exec-line was necessary:
Exec=/media/mmcblk0p1/Programs/_lua/bin/lua /media/mmcblk0p1/Programs/_lua/scripts/run_debug.lua
instead of Exec=/media/mmcblk0p1/Programs/_lua/scripts/run_debug.lua
Now I could have tested MiniPad and Toolbox. Both shows the same problem:
sh: /media/mmcblk0p1/Programs/tests/_code/minipad.sh
: not found
BTW - is it possible to make the "selection"-window (where you select path or the program) bigger in RunDebug? It is veeery small...
