What does the cryptic crossword clue "Cracking clue in fundamental parts (6)" mean?

The wordplay uses an anagram. anagram of IN (synonym="IN") + CLUE (synonym="CLUE") = NUCLEI The answer is NUCLEI.

Cracking clue in fundamental parts (6)

Guardian Cryptic #26527 | 6 Down | 2015-03-24 flower