I do not have your data to fully understand your problem. Typing “naha” in the word filter should find all the words that begin with “naha”. There is a setting to find something at the end of words.
Go to the Wordlist menu Sort by → End of word
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Then type the character string you are looking for in the word filter. (I will use “aga”) for this data.
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To have more control you will have to search using the normal Find function, then you can specify “Beginning of the word”, “End of the word” and “ignore diacritics”. you will have to jump to the verse to make any changes, but you would be able to see only words with “naha” at the beginning or the end of words. For even more control over the final list you would have to use RegexPal.
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Unfortunately, the powerful searching features of Find are not also in the Wordlist tool. Might be a good feature request.