docs: restructure into topic subdirectories, collapse duplicated index

Per mara's go-ahead on hyperhive#3902 ("getting started is good, but
terminal rendering does not go in there i think"):

Moved 21 top-level docs/*.md files into 7 new topic subdirectories
(existing web-ui/, turn-loop/, swarm/, tools/, crates/ untouched):
  getting-started/  setup.md
  agent-lifecycle/  agent-hierarchy.md, approvals.md, persistence.md
  trust-boundary/   boundary.md, security.md
  integrations/     forge.md, matrix.md, github.md, knowledge.md
  networking/       gateway.md, network.md, snapshot-store.md
  scheduler/        jobq.md, coordinator.md, ci.md, observability.md
  process/          conventions.md, gotchas.md, pr-review-gate.md
  web-ui/           terminal-rendering.md (moved into the EXISTING dir,
                    per mara's correction to the original getting-started
                    guess -- it's UI implementation detail, not onboarding)

The physical layout now matches docs/README.md's own topical headers,
which already amounted to this taxonomy -- see the scoping comment on
the issue for the two findings that motivated this (a genuine
duplication between CLAUDE.md's old "Reading paths" list and
docs/README.md's grouped one, since drifted out of sync with each
other; and the flat layout not matching the grouping we already had).

Fixed every cross-reference this moved across the whole repo (~120
files: docs/ internal links at every depth, Rust doc comments, nix
module option docs, crate READMEs) -- verified two ways: a grep sweep
confirming zero remaining references to any old path, and a script
that resolves every markdown link in docs/**/*.md + CLAUDE.md +
README.md against the filesystem and reports anything that doesn't
exist (zero broken links).

Collapsed CLAUDE.md's "Reading paths" section (the duplicate) down to
a pointer at docs/README.md, now the single index. Rewrote
docs/README.md itself to use the new subdirectory paths and added the
one doc it was missing that CLAUDE.md's old copy had (pr-review-gate.md).

Classified all 22 docs/*.md files first via a haiku subagent (mara's
suggestion) on two axes -- proposed grouping and operator-vs-
implementation focus -- before finalizing the taxonomy; spot-checked
the report and found internal inconsistencies (its classification
table disagreed with its own summary section for a few files), so this
taxonomy is my original proposal + the one correction mara gave
directly, not a blind application of the subagent's table. The
operator-focus data it gathered is still useful for a follow-up
content pass (docs skewing 'mixed' rather than pure operator-facing),
not addressed in this PR -- structure only.

nix fmt clean, both pre-push lints clean.

docs/turn-loop/README.md

@@ -14,7 +14,7 @@ agents) runs:
    queued and unacked, so a resume drains the backlog instead of
    losing it; reminders and todo wakes buffer in their channels. Set
    it with `hivectl agent <name> pause` or the dashboard toggle; see
-   [persistence](../persistence.md#-harnesspaused-per-agent).
+   [persistence](../agent-lifecycle/persistence.md#-harnesspaused-per-agent).
 1. Long-poll `Recv` on its socket. The host-side broker
    (`broker.rs::recv_blocking_batch`) returns immediately if there's
    a pending message, otherwise waits up to 30 s for a broker `Sent`
@@ -91,21 +91,21 @@ doc for the trait shape.
 `serve_main` reads `HIVE_PORT` (default `DEFAULT_WEB_PORT`) +
 `HIVE_LABEL` (default `"hive"` for standalone runs; the meta
 flake sets it unconditionally for any container-deployed agent;
-see `docs/conventions.md::Hive identity` for the env stack),
+see `docs/process/conventions.md::Hive identity` for the env stack),
 opens turn-stats sqlite, prepares the on-boot files (see
 [claude-invocation](claude-invocation.md#on-boot-files)),
 installs claude plugins, spawns `web_ui::serve` + `vacuum::run`,
 and either drops into `serve_loop` directly (`Online`) or parks on
 the login flow first (`NeedsLogin`). Forge notifications are polled by
 their own process, not this loop — see `hive-forge-notify` in
-[`forge.md`](../forge.md).
+[`forge.md`](../integrations/forge.md).
 
 Boot also opens the todos store and the socket in-container producers
 dial. Matrix / bash / forge-notify daemons and the in-process
 `disk_watch` todo producer (low state-disk space) are the built-in
 producers, but the socket accepts any `subsystem` marker — a
 user-configured MCP server can push its own todos the same way. See
-[`docs/persistence.md`](../persistence.md#state-dirs-per-agent) for
+[`docs/agent-lifecycle/persistence.md`](../agent-lifecycle/persistence.md#state-dirs-per-agent) for
 what each built-in todo producer watches and how the store + `get_loose_ends`
 merge work.
 

docs/turn-loop/claude-invocation.md

@@ -31,7 +31,7 @@ this package moves fast, the operator can pin one hive-wide with
 into each agent's flake, and `claude` on PATH becomes a symlink to it
 instead of the container's own `claude-code` — so there's only ever one
 `claude` in the container. Agents pick up a new build on their
-next rebuild, not live. See docs/gotchas.md::`claude-code` is unfree.
+next rebuild, not live. See docs/process/gotchas.md::`claude-code` is unfree.
 
 Hive-enforced settings ship at `/etc/claude-code/managed-settings.json`
 (claude-code's canonical managed-settings path — precedence #1,

docs/turn-loop/config.md

@@ -59,7 +59,7 @@ sudo rejection rather than silently succeeding — easier to audit.
 
 `hyperhive.user.uid`, `hyperhive.user.gid`, and
 `hyperhive.user.name` are the companion options; see
-`docs/agent-hierarchy.md` — "Harness systemd unit shape" for the full
+`docs/agent-lifecycle/agent-hierarchy.md` — "Harness systemd unit shape" for the full
 `user.*` surface.
 
 ## Dashboard links
@@ -284,7 +284,7 @@ KEYS
 The file lives in the agent's bind-mounted **harness** dir, not `state/`
 — `harness/` survives container rebuilds exactly like `state/` does, but
 (unlike `state/`) is never bind-mounted into a parent agent's container
-(see `docs/persistence.md`'s "Parent access to child state"), so an API
+(see `docs/agent-lifecycle/persistence.md`'s "Parent access to child state"), so an API
 key placed here is reachable by nothing but this agent and the host.
 
 ⚠️ Verified end-to-end against OpenRouter has not happened as of this

docs/turn-loop/mcp.md

@@ -70,7 +70,7 @@ which still wakes a turn (the todo-wake path — see [Turn
 outcomes](README.md#turn-outcomes)) but via a generic "call
 `get_loose_ends`" prompt rather than the event body itself. Full
 payload shapes and routing logic in
-[`docs/approvals.md` § Helper events](../approvals.md#helper-events-to-the-submitting-agent).
+[`docs/agent-lifecycle/approvals.md` § Helper events](../agent-lifecycle/approvals.md#helper-events-to-the-submitting-agent).
 
 **Inbox** (`inbox` group): `get_loose_ends(agent?)`,
 `cancel_loose_end(kind, id)`, `remind(message, delay_seconds? |
@@ -148,7 +148,7 @@ already in flight.
 - **Capability-gated** — `get_host_journal` (requires
   `read_host_journal` capability set via the P3RM1SS10NS tab;
   orthogonal to tool groups). Full list of capabilities and their
-  effects in [`docs/conventions.md#capabilities`](../conventions.md).
+  effects in [`docs/process/conventions.md#capabilities`](../process/conventions.md).
   Also documented in [`docs/tools/scheduling.md`](../tools/scheduling.md).
 - **Matrix MCP + extra servers** — `mcp__matrix__*` tools and
   per-agent extra MCP config. See