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Here is the solution for Cryptic Crossword 1:

3A The French after taxi line (5)

The in French = LE, after = place after, taxi = CAB ⇒ CABLE = line

6A Scare the final missing presidential killer (5)

Scare = BOO, THe final missing ⇒ BOOTH = presidential killer (John Wilkes Booth)

7A Even Al-Qaeda has boy (3)

Even letters of aLqAeDa ⇒ LAD = boy

8A Incomplete bias (7)

Incomplete = bias ⇒ PARTIAL

9A Lesbian more masculine than slaughterer (7)

Lesbian more masculine = slaughterer = BUTCHER

11A Illness soared, apparently (3)

Soared = FLEW, apparently = homophone ⇒ FLU = Illness

12A Orca travelled north for would be tree (5)

Travelled = anagram of ORCA = ACOR, north = N ⇒ ACORN = would be tree

13A Homes found in Neon streets (5)

Neon = NE, Streets = STS ⇒ NESTS = homes

1D Confused upon brief cure for illness (9)

Confused = anagram of UPONBRIEF ⇒ IBRUPROFEN = cure for illness

2D Reportedly drag swine (4)

Drag = BORE, reportedly = homophone ⇒ BOAR = swine

3D Church heard joint before sung service of festivity (9)

Church = CH, joint = WRIST, heard = homophone of wRIST, service = MASS, sung = homophone of MASs ⇒ CHRISTMAS = festivity

4D Nobel laureate hiding alarm (4)

Hiding = hidden word in noBEL Laureate ⇒ BELL = alarm

5D Lost encoder in system? (9)

Lost = anagram of ENCODER IN ⇒ Endocrine = type of system (question mark = example of)

9D Taps insects (4)

Taps = Insects ⇒ BUGS

10D Ring famous bear up (4)

Famous bear = POOH, up = reverse ⇒ HOOP = ring