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/turn-loop/mcp.md

@@ -70,7 +70,7 @@ which still wakes a turn (the todo-wake path — see [Turn
 outcomes](README.md#turn-outcomes)) but via a generic "call
 `get_loose_ends`" prompt rather than the event body itself. Full
 payload shapes and routing logic in
-[`docs/approvals.md` § Helper events](../approvals.md#helper-events-to-the-submitting-agent).
+[`docs/agent-lifecycle/approvals.md` § Helper events](../agent-lifecycle/approvals.md#helper-events-to-the-submitting-agent).
 
 **Inbox** (`inbox` group): `get_loose_ends(agent?)`,
 `cancel_loose_end(kind, id)`, `remind(message, delay_seconds? |
@@ -148,7 +148,7 @@ already in flight.
 - **Capability-gated** — `get_host_journal` (requires
   `read_host_journal` capability set via the P3RM1SS10NS tab;
   orthogonal to tool groups). Full list of capabilities and their
-  effects in [`docs/conventions.md#capabilities`](../conventions.md).
+  effects in [`docs/process/conventions.md#capabilities`](../process/conventions.md).
   Also documented in [`docs/tools/scheduling.md`](../tools/scheduling.md).
 - **Matrix MCP + extra servers** — `mcp__matrix__*` tools and
   per-agent extra MCP config. See