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D. Filter setup :
Multifill color: The target color to colorize, white for my lineart.
Threshold: 16 , to also colorize the bright-grey and values near to white.
Use a custom palette: select it
Ignore area inferior or equal to : 0 , we want all zone even the small one to be computed.
Flag Area inferior or equal to: 20 ; the "Flag" concept is a feature of multifill. "Flag Area" are a type of small zones. I setup at 20. Every zone under a bounding box of 20x20px will be considered as "Flag Area".
Flag colour: In my situation, a neutral grey will help for setting up a background for little zones. This neutral grey can stand-for a shadow, or a glass part not really well defined.
Method ( check the flag area size ) : Width and Height
And select the Copy Layer first ( for keeping your original layer safe ) and Flatten after ( to remove the black lines at the end of the process ).
Press OK and let the script work.