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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@ -79,7 +79,7 @@ fn require_privilege() -> Result<()> {
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/// Execs `machinectl shell <name>@h-<name>` running claude as the agent
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/// user from its state dir, reproducing the harness's per-turn claude
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/// invocation (flags, session selection, why it never collides with the
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/// live harness session). See `docs/tools/hivectl.md` (Choom) for the
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/// live harness session). See `docs/2-handbook/tools/hivectl.md` (Choom) for the
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/// full rationale. Inherits the caller's PTY; requires root or `hive-admin`
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/// group membership, plus a running container.
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///
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