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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.
This commit is contained in:
iris 2026-11-06 18:30:12 +01:00 • committed by mara
commit 6739bb903d

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@ -7,7 +7,7 @@
//! Claude credentials live at `$HOME/.claude` (resolves to
//! `/home/<agent-name>/.claude` because the harness service runs as a
//! non-root unix user matching the agent label — see
//! `docs/agent-lifecycle/persistence.md::First-boot agent-user migration`).
//! `docs/2-handbook/agent-lifecycle/persistence.md::First-boot agent-user migration`).
//!
//! All three paths can be overridden via env vars (`HYPERHIVE_STATE_DIR`,
//! `HYPERHIVE_HARNESS_DIR`, `HYPERHIVE_CLAUDE_DIR`) for dev / test scenarios.