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Solution 3 (documentation) can easily be done for existing versions of Python. Any other fix I think would have to be done in the next Python version (3.6).
By solution 2 (dynamically swap histories), do you mean add an API to save and load the entire history list somewhere, like read/write_history_file(), but maybe to a Python list instead?
A variation on solution 4 came to my mind: Add a global variable or function to the readline module to enable or disable automatic history addition. Or maybe a callback that is run after a line is entered, with it set to the current implementation by default.
If I understand solution 5 (new version of call_readline), that also seems reasonable. I guess you mean to add a new function to replace the Python call to input()? A minor downside would be that the caller has to do extra work if it wants to use input() when the Readline library is unavailable.