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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@ -23,7 +23,7 @@ use crate::mcp_config;
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// auto-compaction and its cross-session auto-memory because hyperhive owns those
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// concerns (`/compact` on overflow, notes persistence under `/state`). How the
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// file is wired (the nix asset) + the full rationale live in
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// `docs/turn-loop/claude-invocation.md`. Unknown keys are silently ignored by
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// `docs/4-implementation/turn-loop/claude-invocation.md`. Unknown keys are silently ignored by
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// claude-code; if a key gets renamed we'll spot it because the corresponding
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// behavior will start firing mid-turn again.
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