Companion to the raw-JSON deprecation warning committed on this branch (adds the
smoke coverage that was meant to land with it).
Migrate scripts/smoke-test.sh from raw-JSON `cli <tool> '{...}'` invocations to
FLAG form for every tool (index_repository / search_graph / trace_path /
get_graph_schema / query_graph incl. all Cypher checks / get_architecture /
search_code / delete_project), with identical results verified against a prior
run; flag form passes the Cypher query as one argv token, so the old
JSON-escaping helper is removed. Add dedicated guards for an integer flag
(--limit / --depth), a bare boolean (--exclude-entry-points), a repeated array
flag (--semantic-query -> JSON array), piped stdin, --args-file, and per-tool
--help (RC 0 + shows a flag; unknown tool -> RC!=0), plus the deprecation guard
(raw JSON warns on stderr; flag form does not). Non-CLI phases (incl. Phase 10
binary security) unchanged. Full smoke: ALL PASSED.
Signed-off-by: Martin Vogel <martin.vogel.tech@gmail.com>
Martin Vogel
4a0a9cab90