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Expand smoke-test.sh with Phase 5 (MCP stdio transport), Phase 6 (CLI subcommands: install/uninstall/update --dry-run), and Phase 7 (MCP advanced tool calls: search_code v2, get_code_snippet). Add smoke/smoke-amd64 services to Docker compose that build then run all 7 smoke test phases. Include in run.sh full/all flows. Add python3-minimal to Dockerfile for smoke test JSON parsing. Fix Phase 4a shutdown test to use portable background+kill pattern instead of `timeout` (not available on macOS). Add --dry-run, --standard, --ui flags to update command. Fix clang-tidy readability-implicit-bool-conversion in dry_run ternary.