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/web-ui/dashboard.md

@@ -175,7 +175,7 @@ rides the same row but is fed by a separate ~5 min background `du` sampler
 last-sampled value (`null` until the first sample). Network is intentionally
 omitted — agents share the host netns, so there is no per-container net
 counter (per-agent network needs the netns-isolation roadmap in
-`docs/network.md`).
+`docs/networking/network.md`).
 
 Hive infrastructure services (`hive-ci`, `hive-forge`, `hive-gateway`,
 `hive-matrix`) have no dashboard panel — `hivectl stop`/`start`/`restart`
@@ -362,7 +362,7 @@ account appears only once it has been provisioned through the form.
 ### GITHUB tab
 
 Provision a single per-agent GitHub personal access token (see
-[`docs/github.md`](../github.md) for the injection + `gh`/git-push
+[`docs/integrations/github.md`](../integrations/github.md) for the injection + `gh`/git-push
 mechanics). No login flow — the operator pastes an existing PAT for a
 dedicated bot account, with a security-warning banner (dedicated account +
 minimally-scoped token) and a link to
@@ -640,7 +640,7 @@ the matrix module exposes).
 
 The unified nginx-front re-root to
 `https://chat.${hyperhive.swarm.domain}` + `.well-known/matrix/client`
-auto-discovery lives in `docs/gateway.md` (atlas's lane).
+auto-discovery lives in `docs/networking/gateway.md` (atlas's lane).
 
 ## FL0W page (`/flow.html`)
 
@@ -782,7 +782,7 @@ front (`StateSnapshot.gateway_enabled`, sourced from the
 base URL is `/agent/<name>` (same origin, gateway proxies to the
 per-agent harness — TCP or unix-domain depending on the agent's
 `HIVE_WEB_SOCKET` opt-in, see
-`docs/gateway.md::Per-agent unix-socket upstream`).
+`docs/networking/gateway.md::Per-agent unix-socket upstream`).
 Gateway-off (legacy / local dev): base URL is
 `http://<host>:<container.port>` (direct TCP fallback). Forge
 links resolve against `state.forge_public_url` (sourced from