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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@ -16,7 +16,7 @@ understand or change: what happens between a message landing in the
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inbox and the agent's reply, how the harness bootstraps login/auth,
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how it serves the per-agent web UI, or how turn/event stats get
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recorded. Architecture detail lives in
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[`docs/turn-loop/`](../docs/turn-loop/README.md); this README is just the
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[`docs/turn-loop/`](../docs/4-implementation/turn-loop/README.md); this README is just the
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map of the module tree.
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## Shape
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@ -49,5 +49,5 @@ map of the module tree.
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Siblings: **`hive-agent-mcp`** (the MCP server this loop points the
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agent at every turn) and **`hive-runtime`** (the library a turn runs
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through).
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[`docs/turn-loop/::Harness binary shape`](../docs/turn-loop/README.md#harness-binary-shape)
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[`docs/turn-loop/::Harness binary shape`](../docs/4-implementation/turn-loop/README.md#harness-binary-shape)
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covers all three together.
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