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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@ -9,7 +9,7 @@
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`@import` and bake the palette into every CSS bundle.
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A theme swap touches only `colors.css` (the 16 base16 slots); this
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derivation layer never changes. See docs/web-ui/css-vars.md. */
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derivation layer never changes. See docs/4-implementation/web-ui/css-vars.md. */
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:root {
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--bg: var(--base00);
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--bg-elev: var(--base01); /* elevated surfaces: dropdowns, popovers */
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