New question #297755 on Sikuli:
https://answers.launchpad.net/sikuli/+question/297755

This issue has occurred in 1.1.0 and 1.1.1 on several operating systems (Ubuntu 
14.04 and 15.10, OSX 10.10 and 10.11, Windows 7, 8.1, and 10), and since this 
issue is cross-version and cross-platform I'm certain it's something I'm doing 
wrong and not a bug.

When you change code in the IDE, save, and then hit Run, Sikuli will run the 
version of the program as it existed when the IDE originally loaded.  The only 
way to force the IDE to run any changes is to make the changes, save, hit Run, 
exit the IDE, restart the IDE, and then hit Run again - then (and only then) 
will Sikuli use the new, altered version of the code when it executes.  This is 
annoying because one of my oldest habits is to add in a debug message such as 
popup("The value of the variable in question is " + str(var)), or adding a new 
logging call in order to investigate a bug or verify a change, but every time I 
do, Sikuli runs the old version without the debug statement.

(Occasionally, this process has to be repeated twice, and I'm not certain what 
situations cause this.)

Is there anything I can do different to get the IDE to run altered code without 
having to restart the IDE every time?

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