docs: refresh tutorials, how-to, design, reference, and examples for v0.4.0

Pre-cut documentation pass for the 0.4.0 release, verified against current source.

Corrections:
- fipsctl: stale 'show identities'/'show node' -> 'show status'
  (host-a-service, run-as-unprivileged-user)
- mesh address derivation: first 16 bytes of SHA-256(pubkey) with the leading
  byte set to 0xfd, not a fixed fd97: prefix (reach-mesh-services,
  ipv6-adapter-walkthrough)
- gateway control socket mode 0660 -> 0770 (troubleshoot-gateway)
- Tor example: add advertised_port: 8443 so the published port matches the
  prose (enable-nostr-discovery)
- bloom mesh-size estimate rewritten to the OR-union-of-peer-filters algorithm;
  plus mtu deep-link, gateway pool wording, and a NAT failure-mode line
- examples: delete orphaned nostr-rs-relay config, accept inbound to the local
  8443 TCP listener, fix fd::/8 -> fd00::/8 typos, dotless wireguard alias

Additions:
- new Nym mixnet transport section (fips-transport-layer) and the architecture
  transport list
- new LAN/mDNS discovery section (fips-nostr-discovery)
- reference docs: Nym transport, LAN discovery, and new control/stats surfaces;
  drop ble from the connect transport list

docs/design/fips-architecture.md

@@ -221,9 +221,11 @@ discovery protocol, and error-recovery integration view live in
 ## Transport Abstraction
 
 FIPS treats the communication medium as a pluggable component. UDP,
-TCP, raw Ethernet, Tor, and BLE all implement the same small datagram
-interface (send, receive, report MTU) and feed peers into a single FMP
-routing layer; radio and serial transports are in the planned set.
+TCP, raw Ethernet, Tor, BLE, and Nym all implement the same small
+datagram interface (send, receive, report MTU) and feed peers into a
+single FMP routing layer; radio and serial transports are in the
+planned set. Nym (an outbound-only mixnet transport) and Tor are
+privacy-oriented deployment modes rather than failover paths.
 Multi-transport nodes bridge between networks transparently. The
 transport-layer specification — including per-transport categories,
 the trait surface, the connection model, and implementation status —