docs: refresh stale file paths after store/ reorg + gen_messages rename

generate_messages.py → gen_messages.py and several gem/ headers moved
under gem/store/ (carrier_store.hpp → store/carriers.hpp, etc.);
e84.hpp split into e84_state.hpp.  The guided-tour chapters still
pointed at the old paths — relink them so the deep-link footnotes
resolve.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

docs/00_index.md

@@ -122,7 +122,7 @@ extension points spelled out.
 | # | Title | Covers |
 |---|-------|--------|
 | [30](30_repository_tour.md) | Repository tour | Directory layout, build system, the eight apps, the test suite. |
-| [31](31_spec_as_data_and_codegen.md) | Spec-as-data + codegen | The five YAML files, how `tools/generate_messages.py` turns `messages.yaml` into typed C++. |
+| [31](31_spec_as_data_and_codegen.md) | Spec-as-data + codegen | The five YAML files, how `tools/gen_messages.py` turns `messages.yaml` into typed C++. |
 | [32](32_stores_and_the_data_model.md) | Stores + the data model | `EquipmentDataModel`, every per-domain store (SVIDs, alarms, carriers, substrates, …) and how they compose. |
 | [33](33_transport.md) | Transport | `hsms::Connection` (asio TCP) and `secsi::Protocol` (FSM-only); the strand-threading contract; T-timer wiring. |
 | [34](34_codec_and_sml.md) | Codec + SML | `secs2::Item` variant, `encode`/`decode`, the SML parser and printer, the identifier-wildcard rule. |