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)))) (. .)))
Other faiths have never flourished. 
( ( Other faiths ) ( ( ( have never ) flourished ) . ) )
(ROOT (S (NP (JJ Other) (NNS faiths)) (VP (VBP have) (ADVP (RB never)) (VP (VBN flourished))) (. .)))