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-sh4re/src/approvals.rs

@@ -8,7 +8,7 @@ use hive_types::Ident;
 use serde::{Deserialize, Serialize};
 
 /// One row in the approval queue. `commit_ref` is overloaded per
-/// `kind` — see `docs/approvals.md::Approval kinds (wire shapes)`
+/// `kind` — see `docs/agent-lifecycle/approvals.md::Approval kinds (wire shapes)`
 /// for the encoding table and lifecycle.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Approval {
@@ -39,7 +39,7 @@ pub struct Approval {
 
 /// What action the approval, when granted, will trigger.
 /// Variant-specific payload encoding +  flow lives in
-/// `docs/approvals.md::Approval kinds (wire shapes)`.
+/// `docs/agent-lifecycle/approvals.md::Approval kinds (wire shapes)`.
 #[derive(Debug, Clone, Copy, Default, Serialize, Deserialize, PartialEq, Eq)]
 #[serde(rename_all = "snake_case")]
 pub enum ApprovalKind {
@@ -63,7 +63,7 @@ pub enum ApprovalKind {
     /// sole config-change flow — a manager opens a PR on its
     /// `agent-configs/<agent>` repo and the operator reviews + approves it.
     /// `commit_ref` = PR number; `fetched_sha` = the reviewed PR head
-    /// pinned at submit. See `docs/approvals.md`.
+    /// pinned at submit. See `docs/agent-lifecycle/approvals.md`.
     #[default]
     MergeConfigPr,
 }
@@ -95,7 +95,7 @@ pub enum ApprovalStatus {
     /// Manager withdrew the request before the operator acted on it.
     /// Distinct from `Denied` (operator decision) and `Failed`
     /// (post-approval lifecycle error). See
-    /// `docs/approvals.md::Withdrawing a pending approval`.
+    /// `docs/agent-lifecycle/approvals.md::Withdrawing a pending approval`.
     Cancelled,
 }
 

hive-sh4re/src/inbox.rs

@@ -86,7 +86,7 @@ pub struct InboxRow {
 }
 
 /// One delivered message in a `Recv` response.
-/// See `docs/conventions.md::Broker delivery + ack cycle` for the
+/// See `docs/process/conventions.md::Broker delivery + ack cycle` for the
 /// full delivery/ack/requeue story.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct DeliveredMessage {
@@ -121,7 +121,7 @@ pub enum ReminderTiming {
 /// thread kinds can land without breaking existing handlers.
 /// Per-flavour scoping + per-variant fields + clock-anomaly
 /// saturation behaviour live in
-/// `docs/conventions.md::Loose-ends wire shape`.
+/// `docs/process/conventions.md::Loose-ends wire shape`.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 #[serde(tag = "kind", rename_all = "snake_case")]
 pub enum LooseEnd {
@@ -190,7 +190,7 @@ pub enum LooseEnd {
 
 /// Kind discriminator for `CancelLooseEnd`. Per-kind store +
 /// authorisation rules live in
-/// `docs/conventions.md::Loose-ends wire shape`.
+/// `docs/process/conventions.md::Loose-ends wire shape`.
 #[derive(Debug, Clone, Copy, Serialize, Deserialize, PartialEq, Eq)]
 #[serde(rename_all = "snake_case")]
 pub enum CancelLooseEndKind {

hive-sh4re/src/manager.rs

@@ -60,7 +60,7 @@ pub fn trusted_sender(s: &str) -> Ident {
 /// Out-of-band events the host-side daemon pushes to the manager's inbox.
 /// Serialised as JSON in `Message::body` (sender = `SYSTEM_SENDER`).
 /// Per-variant triggers + the optional `sha`/`tag` semantics live in
-/// `docs/approvals.md::Helper events to the manager`.
+/// `docs/agent-lifecycle/approvals.md::Helper events to the manager`.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 #[serde(tag = "event", rename_all = "snake_case")]
 pub enum HelperEvent {

hive-sh4re/src/permissions.rs

@@ -11,7 +11,7 @@ use serde::{Deserialize, Serialize};
 /// `snake_case` group names written by the meta renderer from per-agent
 /// config) and expands it to the matching tool names for `--allowedTools`.
 /// When the env var is absent the harness falls back to `AGENT_DEFAULT`.
-/// See `docs/conventions.md::Tool groups`.
+/// See `docs/process/conventions.md::Tool groups`.
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
 #[serde(rename_all = "snake_case")]
 pub enum ToolGroup {
@@ -200,7 +200,7 @@ impl ToolGroup {
 /// Injected into containers as `HIVE_CAPABILITIES` (comma-separated
 /// `snake_case`) via `meta::render_flake`. The harness reads this to
 /// conditionally register capability-gated MCP tools so claude only
-/// sees tools it can actually invoke. See `docs/conventions.md::Capabilities`.
+/// sees tools it can actually invoke. See `docs/process/conventions.md::Capabilities`.
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
 #[serde(rename_all = "snake_case")]
 pub enum Capability {