Etymology
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ur- 
prefix meaning "original, earliest, primitive," from German ur- "out of, original," from Proto-Germanic *uz- "out," from PIE *ud- "up, out" (see out (adv.)) At first only in words borrowed from German (such as ursprache "hypothetical primitive language"); since mid-20c. a living prefix in English. Compare also Urschleim under protoplasm and Urquell under Pilsner.
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proto- 

before vowels prot-, word-forming element in compounds of Greek origin meaning "first, source, parent, preceding, earliest form, original, basic," from Greek prōto-, from prōtos "first" (from PIE *pre-, from root *per- (1) "forward," hence "before, first"). It is also used in forming words in the sciences and to form compounds having historical reference (such as Proto-Indo-European).

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ap- (1)
form of Latin ad- in compounds with words or stems beginning in -p-; see ad-. In Old French reduced to a-, but scribal re-doubling of ap- to app- in imitation of Latin began 14c. in France, 15c. in England, and was extended to some compounds formed in Old French or Middle English that never had a Latin original (appoint, appall).

In words from Greek, ap- is the form of apo before a vowel (see apo-).
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sub- 
word-forming element meaning "under, beneath; behind; from under; resulting from further division," from Latin preposition sub "under, below, beneath, at the foot of," also "close to, up to, towards;" of time, "within, during;" figuratively "subject to, in the power of;" also "a little, somewhat" (as in sub-horridus "somewhat rough"), from PIE *(s)up- (perhaps representing *ex-upo-), a variant form of the root *upo "under," also "up from under." The Latin word also was used as a prefix and in various combinations.

In Latin assimilated to following -c-, -f-, -g-, -p-, and often -r- and -m-. In Old French the prefix appears in the full Latin form only "in learned adoptions of old Latin compounds" [OED], and in popular use it was represented by sous-, sou-; as in French souvenir from Latin subvenire, souscrire (Old French souzescrire) from subscribere, etc.

The original meaning is now obscured in many words from Latin (suggest, suspect, subject, etc.). The prefix is active in Modern English, sometimes meaning "subordinate" (as in subcontractor); "inferior" (17c., as in subhuman); "smaller" (18c.); "a part or division of" (c. 1800, as in subcontinent).
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re- 

word-forming element meaning "back, back from, back to the original place;" also "again, anew, once more," also conveying the notion of "undoing" or "backward," etc. (see sense evolution below), c. 1200, from Old French re- and directly from Latin re- an inseparable prefix meaning "again; back; anew, against."

Watkins (2000) describes this as a "Latin combining form conceivably from Indo-European *wret-, metathetical variant of *wert- "to turn." De Vaan says the "only acceptable etymology" for it is a 2004 explanation which reconstructs a root in PIE *ure "back."

In earliest Latin the prefix became red- before vowels and h-, a form preserved in redact, redeem, redolent, redundant, redintegrate, and, in disguise, render (v.). In some English words from French and Italian re- appears as ra- and the  following consonant is often doubled (see rally (v.1)).

The many meanings in the notion of "back" give re- its broad sense-range: "a turning back; opposition; restoration to a former state; "transition to an opposite state." From the extended senses in "again," re- becomes "repetition of an action," and in this sense it is extremely common as a formative element in English, applicable to any verb. OED writes that it is "impossible to attempt a complete record of all the forms resulting from its use," and adds that "The number of these is practically infinite ...."   

Often merely intensive, and in many of the older borrowings from French and Latin the precise sense of re- is forgotten, lost in secondary senses, or weakened beyond recognition, so that it has no apparent semantic content (receive, recommend, recover, reduce, recreate, refer, religion, remain, request, require). There seem to have been more such words in Middle English than after, e.g. recomfort (v.) "to comfort, console; encourage;" recourse (n.) "a process, way, course." Recover in Middle English also could mean "obtain, win" (happiness, a kingdom, etc.) with no notion of getting something back, also "gain the upper hand, overcome; arrive at;" also consider the legal sense of recovery as "obtain (property) by judgment or legal proceedings." 

And, due to sound changes and accent shifts, re- sometimes entirely loses its identity as a prefix (rebel, relic, remnant, restive, rest (n.2) "remainder," rally (v.1) "bring together"). In a few words it is reduced to r-, as in ransom (a doublet of redemption), rampart, etc.

It was used from Middle English in forming words from Germanic as well as Latin elements (rebuild, refill, reset, rewrite), and was used so even in Old French (regret, regard, reward, etc.).

Prefixed to a word beginning with e, re- is separated by a hyphen, as re-establish, re-estate, re-edify, etc. ; or else the second e has a dieresis over it: as, reëstablish, reëmbark, etc. The hyphen is also sometimes used to bring out emphatically the sense of repetition or iteration : as, sung and re-sung. The dieresis is not used over other vowels than e when re is prefixed : thus, reinforce, reunite, reabolish. [Century Dictionary, 1895]
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