Add smoke tests to Docker test infra + CI pipeline

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.

Author: DeusData

scripts/smoke-test.sh

@@ -177,15 +177,23 @@ cat > "$SHUTDOWN_TMPDIR/input.jsonl" << 'JSONL'
 {"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}
 JSONL
 
-# Run binary with EOF and check it exits within 5 seconds
-timeout 5 "$BINARY" < "$SHUTDOWN_TMPDIR/input.jsonl" > /dev/null 2>&1 || true
-EXIT_CODE=$?
-rm -rf "$SHUTDOWN_TMPDIR"
-
-if [ "$EXIT_CODE" -eq 124 ]; then
+# Run binary with EOF and wait up to 5 seconds (portable — no `timeout` needed)
+"$BINARY" < "$SHUTDOWN_TMPDIR/input.jsonl" > /dev/null 2>&1 &
+SHUTDOWN_PID=$!
+SHUTDOWN_WAITED=0
+while kill -0 "$SHUTDOWN_PID" 2>/dev/null && [ "$SHUTDOWN_WAITED" -lt 5 ]; do
+  sleep 1
+  SHUTDOWN_WAITED=$((SHUTDOWN_WAITED + 1))
+done
+if kill -0 "$SHUTDOWN_PID" 2>/dev/null; then
+  kill "$SHUTDOWN_PID" 2>/dev/null || true
+  wait "$SHUTDOWN_PID" 2>/dev/null || true
+  rm -rf "$SHUTDOWN_TMPDIR"
   echo "FAIL: binary did not exit within 5 seconds after EOF"
   exit 1
 fi
+wait "$SHUTDOWN_PID" 2>/dev/null || true
+rm -rf "$SHUTDOWN_TMPDIR"
 echo "OK: clean shutdown"
 
 # 4b: No residual processes (skip on Windows/MSYS2 where pgrep may not work)
@@ -337,5 +345,89 @@ echo "OK: Content-Length framing works (OpenCode compatible)"
 
 rm -f "$MCP_CL_INPUT" "$MCP_CL_OUTPUT" "$MCP_TOOL_INPUT" "$MCP_TOOL_OUTPUT"
 
+echo ""
+echo "=== Phase 6: CLI subcommands ==="
+
+# 6a: install --dry-run -y
+echo "--- Phase 6a: install --dry-run ---"
+INSTALL_OUT=$("$BINARY" install --dry-run -y 2>&1)
+if ! echo "$INSTALL_OUT" | grep -qi 'install\|skill\|mcp\|agent'; then
+  echo "FAIL: install --dry-run produced unexpected output"
+  echo "$INSTALL_OUT"
+  exit 1
+fi
+if ! echo "$INSTALL_OUT" | grep -qi 'dry-run'; then
+  echo "FAIL: install --dry-run did not indicate dry-run mode"
+  exit 1
+fi
+echo "OK: install --dry-run completed"
+
+# 6b: uninstall --dry-run -y
+echo "--- Phase 6b: uninstall --dry-run ---"
+UNINSTALL_OUT=$("$BINARY" uninstall --dry-run -y 2>&1)
+if ! echo "$UNINSTALL_OUT" | grep -qi 'uninstall\|remov'; then
+  echo "FAIL: uninstall --dry-run produced unexpected output"
+  echo "$UNINSTALL_OUT"
+  exit 1
+fi
+echo "OK: uninstall --dry-run completed"
+
+# 6c: update --dry-run --standard -y
+echo "--- Phase 6c: update --dry-run ---"
+UPDATE_OUT=$("$BINARY" update --dry-run --standard -y 2>&1)
+if ! echo "$UPDATE_OUT" | grep -qi 'dry-run'; then
+  echo "FAIL: update --dry-run did not indicate dry-run mode"
+  echo "$UPDATE_OUT"
+  exit 1
+fi
+if ! echo "$UPDATE_OUT" | grep -qi 'standard'; then
+  echo "FAIL: update --dry-run did not respect --standard flag"
+  exit 1
+fi
+echo "OK: update --dry-run --standard completed"
+
+# 6d: config set/get/reset round-trip
+echo "--- Phase 6d: config set/get/reset ---"
+"$BINARY" config set auto_index true 2>/dev/null
+CONFIG_VAL=$("$BINARY" config get auto_index 2>/dev/null)
+if ! echo "$CONFIG_VAL" | grep -q 'true'; then
+  echo "FAIL: config get auto_index returned '$CONFIG_VAL', expected 'true'"
+  exit 1
+fi
+"$BINARY" config reset auto_index 2>/dev/null
+echo "OK: config set/get/reset round-trip"
+
+echo ""
+echo "=== Phase 7: MCP advanced tool calls ==="
+
+# 7a: search_code via MCP (graph-augmented v2)
+echo "--- Phase 7a: search_code via MCP ---"
+MCP_SC_INPUT=$(mktemp)
+MCP_SC_OUTPUT=$(mktemp)
+cat > "$MCP_SC_INPUT" << SCEOF
+{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"smoke","version":"1.0"}}}
+{"jsonrpc":"2.0","method":"notifications/initialized"}
+{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"index_repository","arguments":{"repo_path":"$TMPDIR","mode":"fast"}}}
+{"jsonrpc":"2.0","id":3,"method":"tools/call","params":{"name":"search_code","arguments":{"pattern":"compute","mode":"compact","limit":3}}}
+{"jsonrpc":"2.0","id":4,"method":"tools/call","params":{"name":"get_code_snippet","arguments":{"qualified_name":"compute"}}}
+SCEOF
+
+mcp_run "$MCP_SC_INPUT" "$MCP_SC_OUTPUT" 30
+
+if ! grep -q '"id":3' "$MCP_SC_OUTPUT"; then
+  echo "FAIL: search_code response (id:3) missing"
+  exit 1
+fi
+echo "OK: search_code v2 via MCP"
+
+# 7b: get_code_snippet via MCP
+if ! grep -q '"id":4' "$MCP_SC_OUTPUT"; then
+  echo "FAIL: get_code_snippet response (id:4) missing"
+  exit 1
+fi
+echo "OK: get_code_snippet via MCP"
+
+rm -f "$MCP_SC_INPUT" "$MCP_SC_OUTPUT"
+
 echo ""
 echo "=== smoke-test: ALL PASSED ==="

src/cli/cli.c

@@ -258,17 +258,34 @@ int cbm_copy_file(const char *src, const char *dst) {
     return rc == 0 ? 0 : -1;
 }
 
-/* Replace a binary file: unlink first (handles read-only existing files),
- * then create with the given data and permissions. */
+/* Replace a binary file. Unlinks the old file first (handles read-only and
+ * running binaries on Unix where unlink succeeds on open files). On all
+ * platforms, the caller should tell the user to restart after update. */
 int cbm_replace_binary(const char *path, const unsigned char *data, int len, int mode) {
     if (!path || !data || len <= 0) {
         return -1;
     }
 
-    /* Remove existing file first — handles the case where the old binary
-     * has no write permission (e.g., 0500). unlink() only requires write
-     * permission on the parent directory, not the file itself. */
-    (void)cbm_unlink(path);
+    /* Remove existing file if it exists. On Unix, unlink works even if the
+     * binary is running (inode stays alive until the process exits). On Windows,
+     * unlink fails on running .exe — rename it aside as fallback. */
+    struct stat st_check;
+    if (stat(path, &st_check) == 0) {
+        /* File exists — remove or rename it */
+        if (cbm_unlink(path) != 0) {
+#ifdef _WIN32
+            /* Windows: can't unlink running .exe — rename aside */
+            char old_path[1024];
+            snprintf(old_path, sizeof(old_path), "%s.old", path);
+            (void)cbm_unlink(old_path);
+            if (rename(path, old_path) != 0) {
+                return -1;
+            }
+#else
+            return -1;
+#endif
+        }
+    }
 
 #ifndef _WIN32
     int fd = open(path, O_WRONLY | O_CREAT | O_TRUNC, (mode_t)mode);
@@ -281,6 +298,7 @@ int cbm_replace_binary(const char *path, const unsigned char *data, int len, int
         return -1;
     }
 #else
+    (void)mode;
     FILE *f = fopen(path, "wb");
     if (!f) {
         return -1;
@@ -2705,6 +2723,18 @@ int cbm_cmd_uninstall(int argc, char **argv) {
 int cbm_cmd_update(int argc, char **argv) {
     parse_auto_answer(argc, argv);
 
+    bool dry_run = false;
+    int variant_flag = 0; /* 0 = ask, 1 = standard, 2 = ui */
+    for (int i = 0; i < argc; i++) {
+        if (strcmp(argv[i], "--dry-run") == 0) {
+            dry_run = true;
+        } else if (strcmp(argv[i], "--standard") == 0) {
+            variant_flag = 1;
+        } else if (strcmp(argv[i], "--ui") == 0) {
+            variant_flag = 2;
+        }
+    }
+
     const char *home = cbm_get_home_dir();
     if (!home) {
         fprintf(stderr, "error: HOME not set (use USERPROFILE on Windows)\n");
@@ -2734,29 +2764,39 @@ int cbm_cmd_update(int argc, char **argv) {
         printf("Found %d existing index(es) that must be rebuilt after update:\n", index_count);
         cbm_list_indexes(home);
         printf("\n");
-        if (!prompt_yn("Delete these indexes and continue with update?")) {
-            printf("Update cancelled.\n");
-            return 1;
+        if (!dry_run) {
+            if (!prompt_yn("Delete these indexes and continue with update?")) {
+                printf("Update cancelled.\n");
+                return 1;
+            }
+            int removed = cbm_remove_indexes(home);
+            printf("Removed %d index(es).\n\n", removed);
+        } else {
+            printf("(dry-run — indexes would be deleted)\n\n");
         }
-        int removed = cbm_remove_indexes(home);
-        printf("Removed %d index(es).\n\n", removed);
     }
 
-    /* Step 2: Ask for UI variant */
-    printf("Which binary variant do you want?\n");
-    printf("  1) standard  — MCP server only\n");
-    printf("  2) ui        — MCP server + embedded graph visualization\n");
-    printf("Choose (1/2): ");
-    (void)fflush(stdout);
-
-    char choice[16];
-    if (!fgets(choice, sizeof(choice), stdin)) {
-        fprintf(stderr, "error: failed to read input\n");
-        return 1;
+    /* Step 2: Determine variant (--standard / --ui flags skip interactive prompt) */
+    bool want_ui = false;
+    if (variant_flag == 1) {
+        want_ui = false;
+    } else if (variant_flag == 2) {
+        want_ui = true;
+    } else {
+        printf("Which binary variant do you want?\n");
+        printf("  1) standard  — MCP server only\n");
+        printf("  2) ui        — MCP server + embedded graph visualization\n");
+        printf("Choose (1/2): ");
+        (void)fflush(stdout);
+
+        char choice[16];
+        if (!fgets(choice, sizeof(choice), stdin)) {
+            fprintf(stderr, "error: failed to read input\n");
+            return 1;
+        }
+        want_ui = (choice[0] == '2');
     }
     // NOLINTNEXTLINE(readability-implicit-bool-conversion)
-    bool want_ui = (choice[0] == '2') ? true : false;
-    // NOLINTNEXTLINE(readability-implicit-bool-conversion)
     const char *variant = want_ui ? "ui-" : "";
     // NOLINTNEXTLINE(readability-implicit-bool-conversion)
     const char *variant_label = want_ui ? "ui" : "standard";
@@ -2779,9 +2819,23 @@ int cbm_cmd_update(int argc, char **argv) {
                  os, arch, ext);
     }
 
-    printf("\nDownloading %s binary for %s/%s ...\n", variant_label, os, arch);
+    if (dry_run) {
+        printf("\nWould download %s binary for %s/%s ...\n", variant_label, os, arch);
+    } else {
+        printf("\nDownloading %s binary for %s/%s ...\n", variant_label, os, arch);
+    }
     printf("  %s\n", url);
 
+    if (dry_run) {
+        printf("\n(dry-run — skipping download, extraction, and binary replacement)\n");
+        printf("  target: %s/.local/bin/codebase-memory-mcp\n", home);
+        printf("  variant: %s\n", variant_label);
+        printf("  os/arch: %s/%s\n", os, arch);
+        printf("\nUpdate dry-run complete.\n");
+        (void)variant;
+        return 0;
+    }
+
     /* Step 4: Download using curl */
     char tmp_archive[256];
     snprintf(tmp_archive, sizeof(tmp_archive), "%s/cbm-update.%s", cbm_tmpdir(), ext);
@@ -2897,6 +2951,7 @@ int cbm_cmd_update(int argc, char **argv) {
 
     printf("\nAll project indexes were cleared. They will be rebuilt\n");
     printf("automatically when you next use the MCP server.\n");
+    printf("\nPlease restart your MCP client to use the new binary.\n");
     (void)variant;
     return 0;
 }

test-infrastructure/Dockerfile

@@ -13,6 +13,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     gcc g++ make \
     zlib1g-dev \
     pkg-config \
+    python3-minimal \
     && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /src

test-infrastructure/docker-compose.yml

@@ -72,6 +72,33 @@ services:
       WINEDEBUG=-all wine64 build/c/test-runner.exe &&
       echo '=== Windows test: OK ==='
 
+  # ── Smoke test (build + run smoke-test.sh) ──────────────────
+  smoke:
+    build:
+      context: ..
+      dockerfile: test-infrastructure/Dockerfile
+    platform: linux/arm64
+    volumes:
+      - ..:/src
+    entrypoint: ["/bin/bash", "-c"]
+    command:
+      - |
+        scripts/build.sh CC=gcc CXX=g++ &&
+        scripts/smoke-test.sh ./build/c/codebase-memory-mcp
+
+  smoke-amd64:
+    build:
+      context: ..
+      dockerfile: test-infrastructure/Dockerfile
+    platform: linux/amd64
+    volumes:
+      - ..:/src
+    entrypoint: ["/bin/bash", "-c"]
+    command:
+      - |
+        scripts/build.sh CC=gcc CXX=g++ &&
+        scripts/smoke-test.sh ./build/c/codebase-memory-mcp
+
   # ── Lint ────────────────────────────────────────────────────
   lint:
     build:

test-infrastructure/run.sh

@@ -26,6 +26,8 @@ case "${1:-full}" in
         echo "=== Linux arm64: test + build ==="
         $COMPOSE run --rm test
         $COMPOSE run --rm build
+        echo "=== Linux arm64: smoke test ==="
+        $COMPOSE run --rm smoke
         echo "=== Windows: cross-compile ==="
         $COMPOSE run --rm build-windows
         echo "=== All passed ==="
@@ -38,6 +40,10 @@ case "${1:-full}" in
         echo "=== Linux arm64: production build (-O2 -Werror) ==="
         $COMPOSE run --rm build
         ;;
+    smoke)
+        echo "=== Linux arm64: smoke test (build + run all 7 phases) ==="
+        $COMPOSE run --rm smoke
+        ;;
     windows)
         echo "=== Windows: cross-compile (mingw-w64) ==="
         $COMPOSE run --rm build-windows
@@ -48,12 +54,14 @@ case "${1:-full}" in
         $COMPOSE run --rm build-amd64
         ;;
     all)
-        echo "=== Linux arm64: test + build ==="
+        echo "=== Linux arm64: test + build + smoke ==="
         $COMPOSE run --rm test
         $COMPOSE run --rm build
-        echo "=== Linux amd64: test + build ==="
+        $COMPOSE run --rm smoke
+        echo "=== Linux amd64: test + build + smoke ==="
         $COMPOSE run --rm test-amd64
         $COMPOSE run --rm build-amd64
+        $COMPOSE run --rm smoke-amd64
         echo "=== Windows: cross-compile ==="
         $COMPOSE run --rm build-windows
         echo "=== All platforms passed ==="
@@ -67,7 +75,7 @@ case "${1:-full}" in
         $COMPOSE run --rm --entrypoint bash test
         ;;
     *)
-        echo "Usage: $0 {full|test|build|windows|amd64|all|lint|shell}"
+        echo "Usage: $0 {full|test|build|smoke|windows|amd64|all|lint|shell}"
         exit 1
         ;;
 esac