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I tried it and it looks like it makes no difference to Matlab.
As long as you set the MAT_F_LOGICAL flag Matlab (2015b) evaluate it as a bool, means:
value = 0 -> false
value != 0 -> true
This behavior works with INT as parameter, too:
Evaluated as bool with value true in Matlab (Octave ignores the flag -> INT16 -> 42)
When reading the value with matio you have to check the flag and then evaluate with the expression given above (value != 0)
Maybe it would be nice to add automatic convertion to matio.
I am actually not sure if the example for MyBoolVariable should use unsigned types (intead of signed) types. You might try it.
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