Clearly, this rosily checkered past was soon to be replaced, chiefly, it seems, as Judeo-Christian-Islamic-Confucian-Buddhist cultures flourished.
( Clearly ( , ( ( ( ( ( ( ( this ( ( rosily checkered ) past ) ) ( ( was soon ) ( to ( be replaced ) ) ) ) , ) ( chiefly ( , ( it seems ) ) ) ) , ) ( as ( ( Judeo-Christian-Islamic-Confucian-Buddhist cultures ) flourished ) ) ) . ) ) )
(ROOT (S (ADVP (RB Clearly)) (, ,) (S (NP (DT this) (ADJP (RB rosily) (JJ checkered)) (NN past)) (VP (VBD was) (ADVP (RB soon)) (S (VP (TO to) (VP (VB be) (VP (VBN replaced))))))) (, ,) (S (ADVP (RB chiefly)) (, ,) (NP (PRP it)) (VP (VBZ seems))) (, ,) (PP (IN as) (NP (NP (JJ Judeo-Christian-Islamic-Confucian-Buddhist) (NNS cultures)) (VP (VBN flourished)))) (. .)))
The bigots did not win with their ignorance. 
( ( The bigots ) ( ( ( did not ) ( win ( with ( their ignorance ) ) ) ) . ) )
(ROOT (S (NP (DT The) (NNS bigots)) (VP (VBD did) (RB not) (VP (VB win) (PP (IN with) (NP (PRP$ their) (NN ignorance))))) (. .)))