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.

hive-c0re/src/workers/agent_sockets.rs

@@ -6,7 +6,7 @@
 //!
 //! Full mechanism — per-agent subdir bind-mount, `hyperhive-socket-bound`
 //! marker gate, gateway UDS upstream, 10s poll loop:
-//! `docs/gateway.md::Per-agent unix-socket upstream`.
+//! `docs/networking/gateway.md::Per-agent unix-socket upstream`.
 
 use std::collections::BTreeMap;
 use std::path::{Path, PathBuf};

hive-c0re/src/workers/auto_update.rs

@@ -14,7 +14,7 @@
 //!    path are skipped — nothing changed, no nix work to do.
 //!
 //! Booting with no config change performs no meta commit — only
-//! reconciles. See `docs/coordinator.md::Boot reconcile`.
+//! reconciles. See `docs/scheduler/coordinator.md::Boot reconcile`.
 
 use std::path::Path;
 use std::sync::Arc;

hive-c0re/src/workers/crash_watch.rs

@@ -1,7 +1,7 @@
 //! Per-container crash and login-state watcher. Polls every managed
 //! container on a 10s interval. Fires `ContainerCrash`, `LoggedIn`,
 //! and `NeedsLogin` helper events. Event semantics and the
-//! `RECENT_TRANSIENT_GRACE` window: `docs/approvals.md::Helper events`.
+//! `RECENT_TRANSIENT_GRACE` window: `docs/agent-lifecycle/approvals.md::Helper events`.
 
 use std::collections::HashSet;
 use std::sync::Arc;

hive-c0re/src/workers/scheduled_prompts_worker.rs

@@ -1,7 +1,7 @@
 //! Background loop that drains due `scheduled_prompts` rows and fans
 //! the body to each active target. 5s poll cadence, shutdown-aware.
 //! Catch-up clamp, missing-target handling, and broker-error retry
-//! semantics: `docs/approvals.md::Scheduled prompt worker`.
+//! semantics: `docs/agent-lifecycle/approvals.md::Scheduled prompt worker`.
 
 use std::sync::Arc;
 use std::time::Duration;