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docs: audit links, glossary, readability pass #2

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eSlider wants to merge 9 commits from docs/improvement into main
pull from: docs/improvement
merge into: :main
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prototype/tsconfig.tsbuildinfo
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{"root":["./src/App.tsx","./src/live.ts","./src/main.tsx","./src/sim.ts","./src/vite-env.d.ts"],"version":"5.9.3"}
{"root":["./src/App.tsx","./src/main.tsx","./src/sim.ts"],"version":"5.9.3"}
simulator/tests/__init__.py
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var/t1/.gitkeep
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var/t3/.gitkeep
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