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/tools/hivectl.md

@@ -6,7 +6,7 @@ admin socket `/run/hyperhive/host.sock`, which is root-only by default —
 so it needs `sudo` unless you grant sudoless access by listing your
 login user in `services.hyperhive.c0re.adminUsers` (adds you to the
 `hive-admin` group that owns the socket; see
-[`docs/boundary.md`](../boundary.md#host-admin-socket-access-hivectl)).
+[`docs/trust-boundary/boundary.md`](../trust-boundary/boundary.md#host-admin-socket-access-hivectl)).
 Available via the `hive-c0re` package in the host NixOS config.
 
 Unlike the `hive-c0re` daemon subcommands (which go through the broker),
@@ -96,7 +96,7 @@ Write an operator-supplied GitHub personal access token (PAT) into an
 agent's token file so its `gh` wrapper + git credential helper can act as
 the bot account. Unlike forge/matrix there is no account creation — the PAT
 is for an existing GitHub account. A CLI alternative to the dashboard
-credentials tab; the [GitHub integration](../github.md) is on by default
+credentials tab; the [GitHub integration](../integrations/github.md) is on by default
 (`hyperhive.github.enable`), so no per-agent config is needed.
 
 ```bash
@@ -108,7 +108,7 @@ hivectl github set-token damocles --token <pat>    # inline (visible in shell hi
   hive-priv — the same credential-injection path as forge/matrix tokens.
   The `gh` wrapper / git credential helper read it live, so a freshly-set
   or rotated PAT takes effect with no rebuild or restart. Refuses an empty
-  token. See [github.md](../github.md) for the full flow + security notes.
+  token. See [github.md](../integrations/github.md) for the full flow + security notes.
 
 ## Gateway
 
@@ -193,7 +193,7 @@ hivectl agent sock set-limits --reset            # drop all overrides
 Overrides the hive-wide `services.hyperhive.agentCpuQuota` /
 `agentMemoryMax` for one agent, persisted to
 `meta/resource-limits.json` (see
-[`persistence.md`](../persistence.md)). Values are systemd's
+[`persistence.md`](../agent-lifecycle/persistence.md)). Values are systemd's
 `CPUQuota=` / `MemoryMax=` syntax: a percentage (`400%` = four full
 cores) for CPU; a size (`8G`), a percentage of physical RAM, or
 `infinity` for memory. Both are validated before they're persisted —
@@ -276,7 +276,7 @@ hivectl agent iris watch    # tail iris's live events; Ctrl-C to stop
 
 Dials the same unix socket the gateway's nginx `proxy_pass`es through
 (`/run/hive-agent/<name>/web.sock` — see [Per-agent unix-socket
-upstream](../gateway.md#per-agent-unix-socket-upstream)) directly and
+upstream](../networking/gateway.md#per-agent-unix-socket-upstream)) directly and
 speaks a bare HTTP/1.1 request for the agent's existing `/events/stream`
 SSE endpoint over it. No gateway hop, no daemon round-trip for the
 stream itself — the daemon socket is only used for the "does this agent
@@ -289,7 +289,7 @@ Prints one compact line per event — reuses the `_icon`/`_summary` fields
 the harness already stamps onto stream-json events for the web UI
 (`stream_enrich.rs`), so tool calls and turn markers read as short
 glyph-prefixed lines instead of raw JSON. Not an attempt at the web
-UI's full collapsible-details rendering (`docs/terminal-rendering.md`)
+UI's full collapsible-details rendering (`docs/web-ui/terminal-rendering.md`)
 — that's presentation for a browser, this is a `tail -f`.
 
 ## Open