Long-lasting stain finally covered by rug — it's coloured (9)
I believe the answer is:
chromatic
'coloured' is the definition.
(associated in meaning)
'long-lasting stain finally covered by rug' is the wordplay.
I cannot really see how this works, but
'by' could be 'at' and 'at' is found in the answer.
The remaining letters 'chromic' is a valid word which might be clued in a way I don't understand.
This may be the basis of the clue (or it may be nonsense).
'it's' acts as a link.
(Other definitions for chromatic that I've seen before include "in colours" , "colourful?" , "Trim coach (anag.)" , "With use of colour" .)