sentences where 'by' is used as an adverb:
He just passed by.
He had already gone by.
I know the only one use of by as an Adverb, ie, the above. INTERNET didn't help me enough.
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In the sentences you mentioned, “by” means “passing a point near something” or “past”. Besides this, “by” as an adverb has two other meanings.
The house is close by.
Away or aside
He put some money by each week for savings.
Adverbs describe the action (verbs). What is by describing here? passed? gone? I am not an expert in grammar but in these sentences, I see "by" as a preposition that is connecting the pronoun "he" and the verbs and is not describing the action "passed" or "gone".