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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@ -88,7 +88,7 @@ fn effort_from(configured: Option<&str>, file: Option<String>) -> (String, Sourc
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// (`hyperhive-rate-limited`, `hyperhive-needs-login`) that grew organically
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// and had no shared schema. A single JSON file is self-documenting, atomic
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// to write, and cheaper for hive-c0re to read on each sweep (one fopen vs
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// two stat calls). See `docs/agent-lifecycle/persistence.md::Harness state files`.
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// two stat calls). See `docs/2-handbook/agent-lifecycle/persistence.md::Harness state files`.
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//
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// Legacy sentinel files written by older harness builds are still honoured
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// by `read_harness_state` so in-place upgrades don't lose state (the new
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