Cryptic crossword clue
Store in pits; it may be one lies neglected if oxygen’s admitted 6

The most common and most likely answer to this crossword clue is the 6 letter word ENSILE

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Buddy explains!

The straight part
We know that "Store in pits" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case store in pits = ensile.
The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.
This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.

What does ENSILE mean?

ENSILE verb
  1. To preserve (forage) in a silo.

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