fix(mcp,ci): harden get_architecture serialization + CodeQL gate

Follow-up to DeusData#281 (handle_get_architecture) plus a CodeQL workflow
upgrade developed in parallel; bundling into one commit because the
test suite had to land alongside both.

mcp.c — handle_get_architecture
- NULL-coerce every const-char* field in the architecture sections
  via `x ? x : ""`, matching the rest of mcp.c (search_graph, etc.).
  Without this, a NULL field becomes a missing JSON key instead of
  an empty string; yyjson_mut_obj_add_str returns false on NULL and
  silently no-ops, so an inconsistent omission could surprise callers.
- Serialize two more architecture aspects that DeusData#281 left on the
  floor: services (cbm_service_link_t: from/to/type/count) and
  clusters (cbm_cluster_info_t: id/label/members/cohesion plus the
  top_nodes / packages / edge_types string arrays). The store-side
  computation populates these for aspects=["all"] / explicit names,
  so dropping them in the serializer was data loss.

tests/test_mcp.c
- New tool_get_architecture_emits_populated_sections regression test.
  Uses a minimal inline fixture (single Function node tagged with
  "is_entry_point": true) since arch_entry_points reads that flag
  out of properties_json. Asserts the response contains both an
  "entry_points" array and the function name — neither would appear
  before DeusData#281 because handle_get_architecture never called
  cbm_store_get_architecture.
- extract_text_content drilled too shallow: it pulled "content" only
  from the JSON root, so it worked for cbm_mcp_handle_tool but
  silently fell through to the raw response for cbm_mcp_server_handle
  (where content lives under .result.content). Added a fallback that
  checks .result.content; both unwrappers tested by existing fixtures.

ci(codeql)
- Run on pull_request to main, not just push; surfaces findings on
  the PR instead of after merge.
- Pull custom queries from ./codeql via `queries: +./codeql`.
- Capture SARIF output and fail the job on any error-level finding,
  using jq to enumerate rule id, file:line, and message text in the
  GitHub Actions error annotation. Warnings are still reported as
  before; only errors block.

Full suite: 2842 passed, 0 failed.

Author: Martin Vogel

.github/workflows/codeql.yml

@@ -15,18 +15,40 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
       - name: Install build dependencies
-        run: sudo apt-get update && sudo apt-get install -y zlib1g-dev
+        run: sudo apt-get update && sudo apt-get install -y zlib1g-dev jq
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@95e58e9a2cdfd71adc6e0353d5c52f41a045d225 # v4
         with:
           languages: c-cpp
           build-mode: manual
+          queries: +./codeql
 
       - name: Build for CodeQL analysis
         run: scripts/build.sh
 
       - name: Perform CodeQL Analysis
+        id: analyze
         uses: github/codeql-action/analyze@95e58e9a2cdfd71adc6e0353d5c52f41a045d225 # v4
         with:
           category: "/language:c-cpp"
+          output: codeql-results
+
+      - name: Fail on CodeQL error-level findings
+        run: |
+          sarif=$(find codeql-results -name '*.sarif' | head -1)
+          if [[ -z "$sarif" ]]; then
+            echo "::error::No SARIF output found"; exit 1
+          fi
+          err=$(jq '[.runs[].results[]? | select((.level // "warning") == "error")] | length' "$sarif")
+          warn=$(jq '[.runs[].results[]? | select((.level // "warning") == "warning")] | length' "$sarif")
+          echo "CodeQL findings: $err error(s), $warn warning(s)"
+          if [[ "$err" -gt 0 ]]; then
+            jq -r '
+              .runs[].results[]?
+              | select((.level // "warning") == "error")
+              | "\(.locations[0].physicalLocation.artifactLocation.uri):\(.locations[0].physicalLocation.region.startLine) [\(.ruleId)] \(.message.text)"
+            ' "$sarif"
+            echo "::error::$err CodeQL error-level finding(s) — failing build."
+            exit 1
+          fi

src/mcp/mcp.c

@@ -1860,7 +1860,8 @@ static char *handle_get_architecture(cbm_mcp_server_t *srv, const char *args) {
         yyjson_mut_val *langs = yyjson_mut_arr(doc);
         for (int i = 0; i < arch.language_count; i++) {
             yyjson_mut_val *item = yyjson_mut_obj(doc);
-            yyjson_mut_obj_add_str(doc, item, "language", arch.languages[i].language);
+            yyjson_mut_obj_add_str(doc, item, "language",
+                                   arch.languages[i].language ? arch.languages[i].language : "");
             yyjson_mut_obj_add_int(doc, item, "file_count", arch.languages[i].file_count);
             yyjson_mut_arr_add_val(langs, item);
         }
@@ -1872,7 +1873,8 @@ static char *handle_get_architecture(cbm_mcp_server_t *srv, const char *args) {
         yyjson_mut_val *pkgs = yyjson_mut_arr(doc);
         for (int i = 0; i < arch.package_count; i++) {
             yyjson_mut_val *item = yyjson_mut_obj(doc);
-            yyjson_mut_obj_add_str(doc, item, "name", arch.packages[i].name);
+            yyjson_mut_obj_add_str(doc, item, "name",
+                                   arch.packages[i].name ? arch.packages[i].name : "");
             yyjson_mut_obj_add_int(doc, item, "node_count", arch.packages[i].node_count);
             yyjson_mut_obj_add_int(doc, item, "fan_in", arch.packages[i].fan_in);
             yyjson_mut_obj_add_int(doc, item, "fan_out", arch.packages[i].fan_out);
@@ -1886,10 +1888,14 @@ static char *handle_get_architecture(cbm_mcp_server_t *srv, const char *args) {
         yyjson_mut_val *eps = yyjson_mut_arr(doc);
         for (int i = 0; i < arch.entry_point_count; i++) {
             yyjson_mut_val *item = yyjson_mut_obj(doc);
-            yyjson_mut_obj_add_str(doc, item, "name", arch.entry_points[i].name);
+            yyjson_mut_obj_add_str(doc, item, "name",
+                                   arch.entry_points[i].name ? arch.entry_points[i].name : "");
             yyjson_mut_obj_add_str(doc, item, "qualified_name",
-                                   arch.entry_points[i].qualified_name);
-            yyjson_mut_obj_add_str(doc, item, "file", arch.entry_points[i].file);
+                                   arch.entry_points[i].qualified_name
+                                       ? arch.entry_points[i].qualified_name
+                                       : "");
+            yyjson_mut_obj_add_str(doc, item, "file",
+                                   arch.entry_points[i].file ? arch.entry_points[i].file : "");
             yyjson_mut_arr_add_val(eps, item);
         }
         yyjson_mut_obj_add_val(doc, root, "entry_points", eps);
@@ -1900,9 +1906,12 @@ static char *handle_get_architecture(cbm_mcp_server_t *srv, const char *args) {
         yyjson_mut_val *routes = yyjson_mut_arr(doc);
         for (int i = 0; i < arch.route_count; i++) {
             yyjson_mut_val *item = yyjson_mut_obj(doc);
-            yyjson_mut_obj_add_str(doc, item, "method", arch.routes[i].method);
-            yyjson_mut_obj_add_str(doc, item, "path", arch.routes[i].path);
-            yyjson_mut_obj_add_str(doc, item, "handler", arch.routes[i].handler);
+            yyjson_mut_obj_add_str(doc, item, "method",
+                                   arch.routes[i].method ? arch.routes[i].method : "");
+            yyjson_mut_obj_add_str(doc, item, "path",
+                                   arch.routes[i].path ? arch.routes[i].path : "");
+            yyjson_mut_obj_add_str(doc, item, "handler",
+                                   arch.routes[i].handler ? arch.routes[i].handler : "");
             yyjson_mut_arr_add_val(routes, item);
         }
         yyjson_mut_obj_add_val(doc, root, "routes", routes);
@@ -1913,9 +1922,12 @@ static char *handle_get_architecture(cbm_mcp_server_t *srv, const char *args) {
         yyjson_mut_val *hotspots = yyjson_mut_arr(doc);
         for (int i = 0; i < arch.hotspot_count; i++) {
             yyjson_mut_val *item = yyjson_mut_obj(doc);
-            yyjson_mut_obj_add_str(doc, item, "name", arch.hotspots[i].name);
+            yyjson_mut_obj_add_str(doc, item, "name",
+                                   arch.hotspots[i].name ? arch.hotspots[i].name : "");
             yyjson_mut_obj_add_str(doc, item, "qualified_name",
-                                   arch.hotspots[i].qualified_name);
+                                   arch.hotspots[i].qualified_name
+                                       ? arch.hotspots[i].qualified_name
+                                       : "");
             yyjson_mut_obj_add_int(doc, item, "fan_in", arch.hotspots[i].fan_in);
             yyjson_mut_arr_add_val(hotspots, item);
         }
@@ -1927,34 +1939,88 @@ static char *handle_get_architecture(cbm_mcp_server_t *srv, const char *args) {
         yyjson_mut_val *boundaries = yyjson_mut_arr(doc);
         for (int i = 0; i < arch.boundary_count; i++) {
             yyjson_mut_val *item = yyjson_mut_obj(doc);
-            yyjson_mut_obj_add_str(doc, item, "from", arch.boundaries[i].from);
-            yyjson_mut_obj_add_str(doc, item, "to", arch.boundaries[i].to);
+            yyjson_mut_obj_add_str(doc, item, "from",
+                                   arch.boundaries[i].from ? arch.boundaries[i].from : "");
+            yyjson_mut_obj_add_str(doc, item, "to",
+                                   arch.boundaries[i].to ? arch.boundaries[i].to : "");
             yyjson_mut_obj_add_int(doc, item, "call_count", arch.boundaries[i].call_count);
             yyjson_mut_arr_add_val(boundaries, item);
         }
         yyjson_mut_obj_add_val(doc, root, "boundaries", boundaries);
     }
 
+    /* Cross-service links (HTTP/async between services) */
+    if (arch.service_count > 0) {
+        yyjson_mut_val *services = yyjson_mut_arr(doc);
+        for (int i = 0; i < arch.service_count; i++) {
+            yyjson_mut_val *item = yyjson_mut_obj(doc);
+            yyjson_mut_obj_add_str(doc, item, "from",
+                                   arch.services[i].from ? arch.services[i].from : "");
+            yyjson_mut_obj_add_str(doc, item, "to",
+                                   arch.services[i].to ? arch.services[i].to : "");
+            yyjson_mut_obj_add_str(doc, item, "type",
+                                   arch.services[i].type ? arch.services[i].type : "");
+            yyjson_mut_obj_add_int(doc, item, "count", arch.services[i].count);
+            yyjson_mut_arr_add_val(services, item);
+        }
+        yyjson_mut_obj_add_val(doc, root, "services", services);
+    }
+
     /* Package layers */
     if (arch.layer_count > 0) {
         yyjson_mut_val *layers = yyjson_mut_arr(doc);
         for (int i = 0; i < arch.layer_count; i++) {
             yyjson_mut_val *item = yyjson_mut_obj(doc);
-            yyjson_mut_obj_add_str(doc, item, "name", arch.layers[i].name);
-            yyjson_mut_obj_add_str(doc, item, "layer", arch.layers[i].layer);
-            yyjson_mut_obj_add_str(doc, item, "reason", arch.layers[i].reason);
+            yyjson_mut_obj_add_str(doc, item, "name",
+                                   arch.layers[i].name ? arch.layers[i].name : "");
+            yyjson_mut_obj_add_str(doc, item, "layer",
+                                   arch.layers[i].layer ? arch.layers[i].layer : "");
+            yyjson_mut_obj_add_str(doc, item, "reason",
+                                   arch.layers[i].reason ? arch.layers[i].reason : "");
             yyjson_mut_arr_add_val(layers, item);
         }
         yyjson_mut_obj_add_val(doc, root, "layers", layers);
     }
 
+    /* Clusters (community detection) */
+    if (arch.cluster_count > 0) {
+        yyjson_mut_val *clusters = yyjson_mut_arr(doc);
+        for (int i = 0; i < arch.cluster_count; i++) {
+            const cbm_cluster_info_t *c = &arch.clusters[i];
+            yyjson_mut_val *item = yyjson_mut_obj(doc);
+            yyjson_mut_obj_add_int(doc, item, "id", c->id);
+            yyjson_mut_obj_add_str(doc, item, "label", c->label ? c->label : "");
+            yyjson_mut_obj_add_int(doc, item, "members", c->members);
+            yyjson_mut_obj_add_real(doc, item, "cohesion", c->cohesion);
+            yyjson_mut_val *top = yyjson_mut_arr(doc);
+            for (int j = 0; j < c->top_node_count; j++) {
+                yyjson_mut_arr_add_str(doc, top, c->top_nodes[j] ? c->top_nodes[j] : "");
+            }
+            yyjson_mut_obj_add_val(doc, item, "top_nodes", top);
+            yyjson_mut_val *pkgs = yyjson_mut_arr(doc);
+            for (int j = 0; j < c->package_count; j++) {
+                yyjson_mut_arr_add_str(doc, pkgs, c->packages[j] ? c->packages[j] : "");
+            }
+            yyjson_mut_obj_add_val(doc, item, "packages", pkgs);
+            yyjson_mut_val *etypes = yyjson_mut_arr(doc);
+            for (int j = 0; j < c->edge_type_count; j++) {
+                yyjson_mut_arr_add_str(doc, etypes, c->edge_types[j] ? c->edge_types[j] : "");
+            }
+            yyjson_mut_obj_add_val(doc, item, "edge_types", etypes);
+            yyjson_mut_arr_add_val(clusters, item);
+        }
+        yyjson_mut_obj_add_val(doc, root, "clusters", clusters);
+    }
+
     /* File tree */
     if (arch.file_tree_count > 0) {
         yyjson_mut_val *file_tree = yyjson_mut_arr(doc);
         for (int i = 0; i < arch.file_tree_count; i++) {
             yyjson_mut_val *item = yyjson_mut_obj(doc);
-            yyjson_mut_obj_add_str(doc, item, "path", arch.file_tree[i].path);
-            yyjson_mut_obj_add_str(doc, item, "type", arch.file_tree[i].type);
+            yyjson_mut_obj_add_str(doc, item, "path",
+                                   arch.file_tree[i].path ? arch.file_tree[i].path : "");
+            yyjson_mut_obj_add_str(doc, item, "type",
+                                   arch.file_tree[i].type ? arch.file_tree[i].type : "");
             yyjson_mut_obj_add_int(doc, item, "children", arch.file_tree[i].children);
             yyjson_mut_arr_add_val(file_tree, item);
         }

tests/test_mcp.c

@@ -525,6 +525,56 @@ TEST(tool_get_architecture_empty) {
     PASS();
 }
 
+/* Regression for #281: handle_get_architecture must actually call
+ * cbm_store_get_architecture and surface its sections. Before the fix
+ * only label/edge histograms were emitted regardless of which aspects
+ * were requested. The store-side arch_entry_points query reads
+ * properties.is_entry_point on Function nodes, so we tag one node and
+ * assert the resulting JSON surfaces an "entry_points" array containing
+ * the tagged function — which is impossible without the wiring. */
+TEST(tool_get_architecture_emits_populated_sections) {
+    cbm_mcp_server_t *srv = cbm_mcp_server_new(NULL);
+    ASSERT_NOT_NULL(srv);
+
+    cbm_store_t *st = cbm_mcp_server_store(srv);
+    ASSERT_NOT_NULL(st);
+
+    const char *proj = "arch-test";
+    cbm_mcp_server_set_project(srv, proj);
+    cbm_store_upsert_project(st, proj, "/tmp/arch-test");
+
+    cbm_node_t main_fn = {0};
+    main_fn.project = proj;
+    main_fn.label = "Function";
+    main_fn.name = "main";
+    main_fn.qualified_name = "arch-test.cmd.main";
+    main_fn.file_path = "cmd/main.go";
+    main_fn.start_line = 1;
+    main_fn.end_line = 3;
+    main_fn.properties_json = "{\"is_entry_point\":true}";
+    ASSERT_GT(cbm_store_upsert_node(st, &main_fn), 0);
+
+    char *resp = cbm_mcp_server_handle(
+        srv, "{\"jsonrpc\":\"2.0\",\"id\":91,\"method\":\"tools/call\","
+             "\"params\":{\"name\":\"get_architecture\","
+             "\"arguments\":{\"project\":\"arch-test\",\"aspects\":[\"all\"]}}}");
+    ASSERT_NOT_NULL(resp);
+    char *inner = extract_text_content(resp);
+    ASSERT_NOT_NULL(inner);
+
+    /* The handler always emits node/edge counts and schema histograms;
+     * those existed before #281. The "entry_points" array only appears
+     * when cbm_store_get_architecture is actually called and its result
+     * is serialized — which is exactly what #281 wires up. */
+    ASSERT_NOT_NULL(strstr(inner, "\"entry_points\""));
+    ASSERT_NOT_NULL(strstr(inner, "main"));
+
+    free(inner);
+    free(resp);
+    cbm_mcp_server_free(srv);
+    PASS();
+}
+
 TEST(tool_query_graph_missing_query) {
     cbm_mcp_server_t *srv = cbm_mcp_server_new(NULL);
 
@@ -1001,6 +1051,13 @@ static char *extract_text_content(const char *mcp_result) {
         return strdup(mcp_result); /* fallback */
     yyjson_val *root = yyjson_doc_get_root(doc);
     yyjson_val *content = yyjson_obj_get(root, "content");
+    if (!content) {
+        /* Handle JSON-RPC wrapper: {"jsonrpc":...,"result":{"content":[...]}} */
+        yyjson_val *rpc_result = yyjson_obj_get(root, "result");
+        if (rpc_result) {
+            content = yyjson_obj_get(rpc_result, "content");
+        }
+    }
     if (!content || !yyjson_is_arr(content)) {
         yyjson_doc_free(doc);
         return strdup(mcp_result);
@@ -1739,6 +1796,7 @@ SUITE(mcp) {
     RUN_TEST(tool_trace_missing_function_name);
     RUN_TEST(tool_delete_project_not_found);
     RUN_TEST(tool_get_architecture_empty);
+    RUN_TEST(tool_get_architecture_emits_populated_sections);
     RUN_TEST(tool_query_graph_missing_query);
 
     /* Pipeline-dependent tool handlers */