fix(config): preserve authored config writes

src/config/io.write-config.test.ts

@@ -313,7 +313,7 @@ describe("config io write", () => {
     });
   });
 
-  it("does not inject include-only $schema into the root config during partial writes", async () => {
+  it("rejects root-include partial writes instead of flattening the root config", async () => {
     await withSuiteHome(async (home) => {
       const configPath = path.join(home, ".openclaw", "openclaw.json");
       const includePath = path.join(home, ".openclaw", "extra.json5");
@@ -328,10 +328,12 @@ describe("config io write", () => {
         `{\n  "$include": "./extra.json5",\n  "gateway": { "mode": "local" }\n}\n`,
         "utf-8",
       );
+      const originalRaw = await fs.readFile(configPath, "utf-8");
 
-      const persisted = await writeGatewayPortAndReadConfig(home, configPath);
-      expect(persisted).not.toHaveProperty("$schema");
-      expect(persisted.gateway).toEqual({ mode: "local", port: 18789 });
+      await expect(writeGatewayPortAndReadConfig(home, configPath)).rejects.toThrow(
+        "Config write would flatten $include-owned config at <root>",
+      );
+      await expect(fs.readFile(configPath, "utf-8")).resolves.toBe(originalRaw);
     });
   });
 

src/config/io.write-prepare.test.ts

@@ -38,6 +38,111 @@ describe("config io write prepare", () => {
     expect(persisted).not.toHaveProperty("sessions.persistence");
   });
 
+  it("preserves authored source-only nested fields during partial writes", () => {
+    const persisted = resolvePersistCandidateForWrite({
+      runtimeConfig: {
+        plugins: {
+          entries: {},
+        },
+      },
+      sourceConfig: {
+        plugins: {
+          entries: {},
+          installs: {
+            "openclaw-web-search": {
+              source: "npm",
+              spec: "@ollama/openclaw-web-search",
+              installPath: "/tmp/openclaw-web-search",
+              resolvedName: "@ollama/openclaw-web-search",
+              resolvedVersion: "0.2.2",
+            },
+          },
+        },
+      },
+      nextConfig: {
+        plugins: {
+          entries: {},
+          installs: {
+            "openclaw-web-search": {
+              source: "npm",
+              spec: "@ollama/openclaw-web-search@0.2.2",
+              installPath: "/tmp/openclaw-web-search",
+              resolvedName: "@ollama/openclaw-web-search",
+              resolvedVersion: "0.2.2",
+            },
+          },
+        },
+      },
+    }) as {
+      plugins?: {
+        installs?: Record<string, Record<string, unknown>>;
+      };
+    };
+
+    expect(persisted.plugins?.installs?.["openclaw-web-search"]).toEqual({
+      source: "npm",
+      spec: "@ollama/openclaw-web-search@0.2.2",
+      installPath: "/tmp/openclaw-web-search",
+      resolvedName: "@ollama/openclaw-web-search",
+      resolvedVersion: "0.2.2",
+    });
+  });
+
+  it("preserves untouched include-owned subtrees during unrelated writes", () => {
+    const persisted = resolvePersistCandidateForWrite({
+      runtimeConfig: {
+        agents: {
+          defaults: { model: "openai/gpt-5.4" },
+        },
+        gateway: { mode: "local" },
+      },
+      sourceConfig: {
+        agents: {
+          defaults: { model: "openai/gpt-5.4" },
+        },
+        gateway: { mode: "local" },
+      },
+      rootAuthoredConfig: {
+        agents: { $include: "./config/agents.json" },
+        gateway: { mode: "local" },
+      },
+      nextConfig: {
+        agents: {
+          defaults: { model: "openai/gpt-5.4" },
+        },
+        gateway: { mode: "local", port: 18789 },
+      },
+    }) as Record<string, unknown>;
+
+    expect(persisted.agents).toEqual({ $include: "./config/agents.json" });
+    expect(persisted.gateway).toEqual({ mode: "local", port: 18789 });
+  });
+
+  it("rejects writes that would flatten include-owned subtrees", () => {
+    expect(() =>
+      resolvePersistCandidateForWrite({
+        runtimeConfig: {
+          agents: {
+            defaults: { model: "openai/gpt-5.4" },
+          },
+        },
+        sourceConfig: {
+          agents: {
+            defaults: { model: "openai/gpt-5.4" },
+          },
+        },
+        rootAuthoredConfig: {
+          agents: { $include: "./config/agents.json" },
+        },
+        nextConfig: {
+          agents: {
+            defaults: { model: "anthropic/sonnet-4.5" },
+          },
+        },
+      }),
+    ).toThrow("Config write would flatten $include-owned config at agents");
+  });
+
   it('formats actionable guidance for dmPolicy="open" without wildcard allowFrom', () => {
     const message = formatConfigValidationFailure(
       "channels.telegram.allowFrom",
@@ -434,26 +539,25 @@ describe("config io write prepare", () => {
     expect(persisted.gateway).toEqual({ mode: "local", port: 18789 });
   });
 
-  it("does not preserve include-only $schema into the root persisted candidate", () => {
+  it("rejects writes that would flatten a root include", () => {
     const sourceConfig = {
       $schema: "https://openclaw.ai/config-from-include.json",
       gateway: { mode: "local" },
     };
 
-    const persisted = resolvePersistCandidateForWrite({
-      runtimeConfig: sourceConfig,
-      sourceConfig,
-      rootAuthoredConfig: {
-        $include: "./extra.json5",
-        gateway: { mode: "local" },
-      },
-      nextConfig: {
-        gateway: { mode: "local", port: 18789 },
-      },
-    }) as Record<string, unknown>;
-
-    expect(persisted).not.toHaveProperty("$schema");
-    expect(persisted.gateway).toEqual({ mode: "local", port: 18789 });
+    expect(() =>
+      resolvePersistCandidateForWrite({
+        runtimeConfig: sourceConfig,
+        sourceConfig,
+        rootAuthoredConfig: {
+          $include: "./extra.json5",
+          gateway: { mode: "local" },
+        },
+        nextConfig: {
+          gateway: { mode: "local", port: 18789 },
+        },
+      }),
+    ).toThrow("Config write would flatten $include-owned config at <root>");
   });
 
   it("does not restore root $schema when the next config explicitly clears it", () => {

src/config/io.write-prepare.ts

@@ -54,6 +54,7 @@ export function projectSourceOntoRuntimeShape(source: unknown, runtime: unknown)
   const next: Record<string, unknown> = {};
   for (const [key, sourceValue] of Object.entries(source)) {
     if (!(key in runtime)) {
+      next[key] = cloneUnknown(sourceValue);
       continue;
     }
     next[key] = projectSourceOntoRuntimeShape(sourceValue, runtime[key]);
@@ -61,6 +62,84 @@ export function projectSourceOntoRuntimeShape(source: unknown, runtime: unknown)
   return next;
 }
 
+function hasOwnIncludeKey(value: unknown): value is Record<string, unknown> {
+  return isRecord(value) && Object.prototype.hasOwnProperty.call(value, "$include");
+}
+
+function collectIncludeOwnedPaths(value: unknown, path: string[] = []): string[][] {
+  if (!isRecord(value)) {
+    return [];
+  }
+  if (hasOwnIncludeKey(value)) {
+    return [path];
+  }
+  return Object.entries(value).flatMap(([key, child]) =>
+    collectIncludeOwnedPaths(child, [...path, key]),
+  );
+}
+
+function patchTouchesPath(patch: unknown, path: string[]): boolean {
+  if (path.length === 0) {
+    return isRecord(patch) ? Object.keys(patch).length > 0 : true;
+  }
+  if (!isRecord(patch)) {
+    return true;
+  }
+  const [head, ...tail] = path;
+  if (!Object.prototype.hasOwnProperty.call(patch, head)) {
+    return false;
+  }
+  return patchTouchesPath(patch[head], tail);
+}
+
+function formatConfigPath(path: string[]): string {
+  return path.length > 0 ? path.join(".") : "<root>";
+}
+
+function getPathValue(value: unknown, path: string[]): unknown {
+  let current = value;
+  for (const segment of path) {
+    if (!isRecord(current)) {
+      return undefined;
+    }
+    current = current[segment];
+  }
+  return current;
+}
+
+function setPathValue(value: unknown, path: string[], nextValue: unknown): unknown {
+  if (path.length === 0) {
+    return cloneUnknown(nextValue);
+  }
+  if (!isRecord(value)) {
+    return value;
+  }
+  const [head, ...tail] = path;
+  return {
+    ...value,
+    [head]: setPathValue(value[head], tail, nextValue),
+  };
+}
+
+function preserveUntouchedIncludes(params: {
+  patch: unknown;
+  rootAuthoredConfig: unknown;
+  persistedCandidate: unknown;
+}): unknown {
+  let next = params.persistedCandidate;
+  for (const includePath of collectIncludeOwnedPaths(params.rootAuthoredConfig)) {
+    if (patchTouchesPath(params.patch, includePath)) {
+      throw new Error(
+        `Config write would flatten $include-owned config at ${formatConfigPath(
+          includePath,
+        )}; edit that include file directly or remove the $include first.`,
+      );
+    }
+    next = setPathValue(next, includePath, getPathValue(params.rootAuthoredConfig, includePath));
+  }
+  return next;
+}
+
 export function resolvePersistCandidateForWrite(params: {
   runtimeConfig: unknown;
   sourceConfig: unknown;
@@ -69,7 +148,11 @@ export function resolvePersistCandidateForWrite(params: {
 }): unknown {
   const patch = createMergePatch(params.runtimeConfig, params.nextConfig);
   const projectedSource = projectSourceOntoRuntimeShape(params.sourceConfig, params.runtimeConfig);
-  const persisted = applyMergePatch(projectedSource, patch);
+  const persisted = preserveUntouchedIncludes({
+    patch,
+    rootAuthoredConfig: params.rootAuthoredConfig ?? params.sourceConfig,
+    persistedCandidate: applyMergePatch(projectedSource, patch),
+  });
   return preserveRootSchemaUri({
     rootAuthoredConfig: params.rootAuthoredConfig ?? params.sourceConfig,
     nextConfig: params.nextConfig,