I am using the Biblical Terms based on stems/roots. If this is what you are interested in, then the answer is that PT is not hierarchic as far as I can see. Unlike AMPLE which is a powerful analyzer that reads from a root dictionary, a prefix dictionary and a suffix dictionary plus rules, PT is simple in that it works from a root/stem indicated in the Wordlist and ignores whatever prefixes and suffixes may be given.
In your example, the root is faŋa. For afaŋa you write a+ faŋa in the morphology column of the Wordlist. For bafaŋa you can write either b+ a+ faŋa or ba+ faŋa. PT only looks for the root/stem and the complete word. How many prefixes and suffixes there are is irrelevant. If you write b+ afaŋa you are telling PT that you have both a root faŋa and a stem afaŋa, so you would need to list both as definitions for thought(s) in the Biblical Terms. If you break down as b+ afaŋa, it cannot find bafaŋa from the root faŋa, only from the stem afaŋa. In my view that is not the best option, so I would write b+ a+ faŋa.
I do mark the various prefixes and suffixes because I like to have a record of the correct morphological breakdown, so a word like musatiinakwaa (their traps) I write as musat +iin +ak +waa (root, class marker, plural marker, possessive.) But PT is only interested in the root musat (which never occurs in this form except as a root in the Wordlist) and the fuil word musatiinakwaa. When musat is given as a definition in the Biblical Terms tool and as long as the words musatiinaa, musatiinak, musatiinacaato, musatiinakaap, musatiiŋwaa, musatiit, musatiitaap are all indicated in the Wordlist with the root musat, PT will happily find all these forms in the Biblical Terms check.
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However, it will not find those places where we use the word for a different Hebrew or Greek term, because the Biblical Terms go by Hebrew words and Hebrew has various words for a trap or snare. So, in the screenshot you should see 8 words from the root musat. However, if I hold the cursor over the vernacular column in the Biblical Terms window I can see that it only found 4 of the 8 words, since the Wordlist is based on the vernacular and the Biblical Terms on the Hebrew/Greek. We also use a different word (stumbling block) for the same Hebrew word. It is complex, because we translate by context, not with word-for-word equivalents.
