Etymology
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over- 

word-forming element meaning variously "above; highest; across; higher in power or authority; too much; above normal; outer; beyond in time, too long," from Old English ofer (from PIE root *uper "over"). Over and its Germanic relations were widely used as prefixes, and sometimes could be used with negative force. This is rare in Modern English, but compare Gothic ufarmunnon "to forget," ufar-swaran "to swear falsely;" Old English ofercræft "fraud."

In some of its uses, moreover, over is a movable element, which can be prefixed at will to almost any verb or adjective of suitable sense, as freely as an adjective can be placed before a substantive or an adverb before an adjective. [OED]

Among the old words not now existing are Old English oferlufu (Middle English oferlufe), literally "over-love," hence "excessive or immoderate love." Over- in Middle English also could carry a sense of "too little, below normal," as in over-lyght "of too little weight" (c. 1400), overlitel "too small" (mid-14c.), overshort, etc.

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-facient 

word-forming element meaning "a doer, one who or that which does," from Latin -facientem (nominative -faciens), combining form of present participle of facere "to make" (from PIE root *dhe- "to set, put").

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hyper- 

word-forming element meaning "over, above, beyond," and often implying "exceedingly, to excess," from Greek hyper (prep. and adv.) "over, beyond, overmuch, above measure," from PIE root *uper "over."

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en- (1)

word-forming element meaning "in; into," from French and Old French en-, from Latin in- "in, into" (from PIE root *en "in"). Typically assimilated before -p-, -b-, -m-, -l-, and -r-. Latin in- became en- in French, Spanish, Portuguese, but remained in- in Italian.

Also used with native and imported elements to form verbs from nouns and adjectives, with a sense "put in or on" (encircle), also "cause to be, make into" (endear), and used as an intensive (enclose). Spelling variants in French that were brought over into Middle English account for parallels such as ensure/insure, and most en- words in English had at one time or another a variant in in-, and vice versa.

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sur- (1)

word-forming element meaning "over, above, beyond, in addition," especially in words from Anglo-French and Old French, from Old French sour-, sor-, sur-, from Latin super "above, over," from PIE root *uper "over."

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pico- 

word-forming element used in making names for very small units of measure, 1915 (formally adopted as a scientific prefix meaning "one trillionth" by the International System of Units, 1960), from Spanish pico "a little over, a small balance," literally "sharp point, beak," a word of Celtic origin (compare Gaulish beccus "beak").

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super- 

word-forming element meaning "above, over, beyond," from Latin super (adverb and preposition) "above, over, on the top (of), beyond, besides, in addition to," from *(s)uper-, variant form of PIE root *uper "over." In English words from Old French, it appears as sur-. The primary sense seems to have shifted over time from usually meaning "beyond" to usually meaning "very much," which can be contradictory. E.g. supersexual, which is attested from 1895 as "transcending sexuality," from 1968 as "very sexual."

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supra- 

word-forming element meaning "above, over, beyond, before," from Latin supra "above, over, before, beyond, on the upper side," in supera (parte), literally "on the upper (side)," from old fem. ablative singular of superus (adj.) "above," related to super "above, over" (from PIE root *uper "over"). In English interchangeable with, but somewhat more technical than, super-. Rare as a prefix in Latin, more common in Medieval Latin, in English chiefly scientific or technical.

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hypso- 

word-forming element meaning "height," from Greek hypsos "height, top," from PIE *upso-, from root *upo "under," also "up from under," hence also "over" The Greek word is cognate with Sanskrit os "above, over," Old Church Slavonic vysoku "high."

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-fy 

word-forming element meaning "make, make into," from French -fier, from Latin -ficare, combining form of facere "to make" (from PIE root *dhe- "to set, put").

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