
Shiny cobweb-like material suggests slug/snail trails, not nematodes (microscopic). Visible worms could be various larvae. Since it's a container, the simplest fix: repot in fresh sterile mix after thoroughly washing roots.
This eliminates whatever's in the soil instantly. Your neem and homemade sprays are fine for foliage pests, but soil issues need a medium replacement.
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Preventing Blossom-End Rot in Tomatoes with Epsom Salts and Solarization
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