The 'tools' (scripts) run by the 'External Tools' plugin allow tools to be defined and active when a GEdit window is open but all text editors are closed. While a tool defined this way shows up in the
    Tools > External Tools > 
sub-menu, when run such a tool does not do anything.

NB. This bug is seen when using beta 3.13.91 on Mac OS X but may apply more broadly.

1) Open GEdit
2) Define a new tool that does a simple 'pwd'
  * Open Tools > Manage External Tools...
  * Click [+] to add a script
  * Change name to 'Ascript'
  * Add as script content:
--------------------------
#!/bin/sh

echo 'Running...'
pwd

--------------------------
  * Change the 'Applicability' to 'Always available'
3) close window

=> The new name shows up in the Tools > External Tools> sub-menu.

4) Open the 'Bottom panel' (from View menu)
5) Run the script from menu [Tools > External Tools > Ascript]

=> The output shows up in the bottom panel

6) Close the empty document with (Command-W or ?Ctrl-W?)

=> The document closes but the window stays open

7) Run the script again from the menu

=> The output window is cleared but now no output appears in the Output panel.

I would expect the script to run given the applicability.

cheers.