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/17_e116_e120_e39_objects.md

@@ -196,7 +196,7 @@ Alarm attribute, or a Process Module attribute.
 ### Code
 
 Handlers live in
-[`include/secsgem/gem/host_command_registry.hpp`](../include/secsgem/gem/host_command_registry.hpp)
+[`include/secsgem/gem/store/host_commands.hpp`](../include/secsgem/gem/store/host_commands.hpp)
 and the generated message catalog.
 
 Tests are bundled into