Cryptic crossword clue
Naval base provides cover in South Africa on run 5,4

The most common and most likely answer to this crossword clue is the 5 plus 4 letter word SCAPA FLOW

I've seen this crossword clue in Financial Times
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Buddy explains!

The straight part
We know that "Naval base" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case naval base = scapa flow.
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.

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