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.

nix/agent-modules/matrix.nix

@@ -166,7 +166,7 @@ in
       loopback-only binding means no auth token is needed (same
       `allowed_hosts` reasoning as `hyperhive.mcp.httpPort`). Safe as a
       single fixed default across all agents (private per-container
-      network namespace — see docs/network.md).
+      network namespace — see docs/networking/network.md).
     '';
   };
 
@@ -229,7 +229,7 @@ in
     # Long-running matrix-sdk client + sync per agent. Serves the MCP
     # tools directly over streamable-http + emits hyperhive wake
     # signals on incoming room events via `/run/hive/mcp.sock`. See
-    # `docs/persistence.md::Matrix per-agent daemon + token-arrival
+    # `docs/agent-lifecycle/persistence.md::Matrix per-agent daemon + token-arrival
     # trigger` for the first-boot-ordering rationale.
     systemd.services.hive-matrix-daemon = lib.mkIf config.hyperhive.matrix.enable {
       description = "long-running matrix-sdk Client + MCP daemon";
@@ -304,7 +304,7 @@ in
     # provisions it after agent containers come up). Without this
     # the daemon would exit 0 silently on first boot and the MCP
     # would have no backend until next restart. See
-    # `docs/persistence.md` (same section as above).
+    # `docs/agent-lifecycle/persistence.md` (same section as above).
     systemd.paths.hive-matrix-daemon = lib.mkIf config.hyperhive.matrix.enable {
       description = "trigger hive-matrix-daemon when a matrix token appears";
       wantedBy = [ "multi-user.target" ];