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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<!-- Selection action bar. Sticky-bottom strip that slides into
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view when one or more agent cards is selected (click the icon
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to toggle). See docs/web-ui/dashboard.md::Selection bar for the bulk
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to toggle). See docs/2-handbook/web-ui/dashboard.md::Selection bar for the bulk
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action gating + clear semantics. -->
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<div
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id="selection-bar"
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