I am using xfce4-terminal on Arch Linux with Geany 1.31-1.  I have my Terminal 
tool path set to
xfce4-terminal -e "/bin/sh %c"
and I have a command bound to Super + T
exo-open --launch TerminalEmulator
When I have a simple C program compiled and press "Run or view the current 
file" in Geany with the Execute command
"./%e"
the program runs in an xfce4-terminal window and prints the standard trailer 
ending in "Press return to continue".  If I then use my Super + T shortcut 
while focused on the terminal window or not to open a new terminal window, the 
window opens so now I have two terminals, one of which was not created by 
Geany.  Pressing the "Run or view the current file" button (which is now a stop 
sign instead of gears) again closes both terminal windows.
However, if I create the other terminal window first by doing Super + T and 
then click the gear button in Geany, the gear button does not change.
I haven't ever looked at Geany's code, but I think this might be caused by 
finding the terminal process to watch by using pgrep or similar, but because 
the child process actually running the program has not fully started it finds 
the existing one and waits for it to close.  I assume this event is monitored 
by having the Geany wrapper script send SIGUSR1 or something like that.  And 
presumably the stop button uses killall or similar thus accidentally killing 
all terminals.  There's a pretty good chance that's totally wrong though :p.

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