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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//! Claude credentials live at `$HOME/.claude` (resolves to
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//! `/home/<agent-name>/.claude` because the harness service runs as a
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//! non-root unix user matching the agent label — see
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//! `docs/agent-lifecycle/persistence.md::First-boot agent-user migration`).
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//! `docs/2-handbook/agent-lifecycle/persistence.md::First-boot agent-user migration`).
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//!
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//! All three paths can be overridden via env vars (`HYPERHIVE_STATE_DIR`,
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//! `HYPERHIVE_HARNESS_DIR`, `HYPERHIVE_CLAUDE_DIR`) for dev / test scenarios.
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