I highly respect what you have written in your website. Why is neshamah used in these 3 references? In the metaphor of the glass-blower, neshamah is the part of man that is most connected to Hashem. Why did Hashem ask Joshua to destroy all who had His breath?
It is an idiom for living human being. That is why it uses the word for the "breath of life" (נשימה) that Hashem used to create Adam (as opposed to the animals. Thus in this case it means every living human being.
And all the spoil of these cities, and the cattle, the children of Israel took for a prey to themselves; but every man they smote with the edge of the sword, until they destroyed them, they did not leave over a soul.
The basic usage is from Brereishis 2:7
וַיִּ֩יצֶר֩ יְהֹוָ֨ה אֱלֹהִ֜ים אֶת־הָֽאָדָ֗ם עָפָר֙ מִן־הָ֣אֲדָמָ֔ה וַיִּפַּ֥ח בְּאַפָּ֖יו נִשְׁמַ֣ת חַיִּ֑ים וַיְהִ֥י הָֽאָדָ֖ם לְנֶ֥פֶשׁ חַיָּֽה:
And the Lord God formed man of dust from the ground, and He breathed into his nostrils the soul of life, and man became a living soul.
and He breathed into his nostrils: He made him of earthly matter and of heavenly matter: the body of earthly matter the soul of heavenly matter. Because on the first day, heaven and earth were created. On the second day, He created the firmament for the heavenly beings; on the third day [He commanded], “and let the dry land appear,” for the earthly beings; on the fourth day, He created luminaries for the heavenly beings; on the fifth day, [He commanded],“Let the waters swarm,” for the earthly beings; on the sixth day, it became necessary to create for both the heavenly and the earthly beings, for if not, there would be jealousy in the Creation, for these would exceed those by the creation of one day. — [from Gen. Rabbah 12:8]
a living soul: Cattle and beasts were also called living souls, but this one of man is the most alive of them all, because he was additionally given intelligence and speech.