why is that "If something has been done a certain way for a long time and has become generally accepted, it's a custom. ", not "If something has been done in a certain way for a long time and has become generally accepted, it's a custom?
If both are correct, why does the first one work?
Those are both correct. "a certain way" (like other similar expressions with "way") can be used adverbially, so it works without the preposition.
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Those are both correct. "a certain way" (like other similar expressions with "way") can be used adverbially, so it works without the preposition.