Why is the Sugyah (discussion) of Chanukah in the Gemarah Shabbos?
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The simplest explanation is the one found in the Gemara -- the section of the Talmud with a nice discussion of what materials make for good oils and wicks is found in Shabbos (vis-a-vis shabbos candles), so it segways from there into what materials to use for Chanukah lighting.
Perhaps a bit deeper, shabbos candles are known as "the home's lights" (ner beiso), whereas Chanukah candles are for the public to see. It's all fine and good that we spread the word to everyone out there (corresponding to the concept of sacred place), but that needs to be firmly rooted in (and can't come at the expense of) ensuring strength and harmony in our personal spheres (corresponding to the concept of sacred time). Thus, chanukah is sandwiched within the laws of shabbos candles.
The Meiri points out that if you only have one candle and it's Friday afternoon of Chanukah, the husband wants to light it outside as a chanukah candle, but the wife wants to light it inside as a shabbos candle; it's not right to leave her in the dark. Similarly the Chofetz Chaim learned from his mentor Reb Nechumka that it's better to wait for your wife to get home and light with her, even if that means later than would otherwise be ideal.
(Based on material heard from Rabbi Aharon Kahn.)