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/01_what_is_secs_gem.md

@@ -237,7 +237,7 @@ layer (`secs2`) which is moved by the transport layer (`hsms` or
 The **codegen** row is worth a footnote: SECS-II has ~160 named
 messages and each one has a typed struct body.  Writing all 160
 builders + parsers by hand would be 5000+ lines of boilerplate, so
-`tools/generate_messages.py` reads `data/messages.yaml` at build time
+`tools/gen_messages.py` reads `data/messages.yaml` at build time
 and emits `messages.hpp` with one typed struct + builder + parser per
 message.  Chapter [31](31_spec_as_data_and_codegen.md) walks through
 how it works.