Remove review-driven protocol cleanup and generic transport changes from this
PR. Keep only stale-session rejection, recovery tests, and the matching
transport documentation; defer valid adjacent findings to follow-up work.
Keep dispatcher details in structured server logs while returning a generic
JSON-RPC internal error to clients. Clarify the session lifecycle docs and
reuse stale-session assertion helpers.
--help printed one flat 35-command list; commands are now grouped by
intent (MCP server; daemon & repositories; query; index; setup) with
internal verbs under Additional Commands. The grouping is assigned once
before Execute and is idempotent.
The docs that still presented the removed 'gortex server' as a run path
now point at 'gortex daemon start --http-addr' (and 'gortex mcp --server'
for the standalone HTTP path), using only real flags.
Andrey Kumanyaev