docs: sort the top-level directories into five sections by what the reader wants
Every docs directory moves under 1-getting-started, 2-handbook, 4-implementation or 5-project; the options reference (section 3) comes from the website and has no directory here. trust-boundary stays whole under the handbook for now. web-ui, swarm and tools split between handbook and implementation, and the command-line references move to 2-handbook/reference. Links, path references in code and nix, and the docs index follow the moves; no page content changes.
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// the `Badge` that opened it (../badge/Badge.tsx) so the control is
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// visually attached to the thing it affects, instead of living three
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// clicks away in a catch-all menu (the junk-drawer pattern
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// `docs/web-ui/design-guide.md` calls out by name). Not a native `<dialog>` — a
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// `docs/5-project/web-ui/design-guide.md` calls out by name). Not a native `<dialog>` — a
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// `showModal()` dialog's backdrop would visually detach it from its
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// anchor badge, and a non-modal `show()` gets no click-outside-to-close
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// for free, so this hand-rolls the same "outside click or Escape
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