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Badly uninstall, losing nuts altogether (2,3)

Ross

I believe the answer is:

in all

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'altogether' is the definition.
(synonyms)

I don't understand how the remainder of the clue works.

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(Other definitions for in all that I've seen before include "after considering everything" , "Taken together" , "totally" , "Everything considered" , "With everything counted" .)

I've seen this clue in The Hindu.
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