Fix stripping of system task settings and projects

Author: ibetitsmike

src/node/config.test.ts

@@ -494,6 +494,28 @@ describe("Config", () => {
       expect(savedRaw.projects).toEqual([["/user/proj", expect.any(Object)]]);
     });
 
+    it("system taskSettings and projects are stripped on save", async () => {
+      writeSystemConfig({
+        taskSettings: { maxConcurrentTasks: 5 },
+        projects: [["/sys/project", { workspaces: [] }]],
+      });
+      writeUserConfig({
+        projects: [["/user/project", { workspaces: [] }]],
+      });
+
+      const loaded = config.loadConfigOrDefault();
+      await config.saveConfig(loaded);
+
+      const savedRaw = JSON.parse(
+        fs.readFileSync(path.join(tempDir, "config.json"), "utf-8")
+      ) as Record<string, unknown>;
+      // System project should not be in saved user config.
+      const savedProjects = savedRaw.projects as Array<[string, unknown]>;
+      const projectPaths = savedProjects.map(([projectPath]) => projectPath);
+      expect(projectPaths).toContain("/user/project");
+      expect(projectPaths).not.toContain("/sys/project");
+    });
+
     it("system object defaults are stripped key-by-key on save", async () => {
       writeSystemConfig({
         featureFlagOverrides: { flagA: "on", flagB: "off" },

src/node/config.ts

@@ -376,16 +376,15 @@ export class Config {
   /**
    * Remove fields from save data that match system config defaults,
    * preventing materialization of admin-managed baselines into user config.
-   * Projects and taskSettings are excluded — projects go through normalization
-   * that changes their shape, and taskSettings always has a default value.
    */
   private stripSystemDefaults(
     data: Record<string, unknown>,
     systemConfig: Partial<AppConfigOnDisk>
   ): void {
     const system = systemConfig as Record<string, unknown>;
     for (const key of Object.keys(data)) {
-      if (key === "projects" || key === "taskSettings") continue;
+      // Projects handled separately below due to array-of-tuples structure.
+      if (key === "projects") continue;
       const dataVal = data[key];
       const sysVal = system[key];
       if (sysVal === undefined) continue;
@@ -420,6 +419,33 @@ export class Config {
         }
       }
     }
+
+    // Strip system-provided projects that haven't been modified.
+    // Projects are arrays of [path, config] tuples — compare by path key.
+    if (Array.isArray(data.projects) && Array.isArray(systemConfig.projects)) {
+      const systemProjectMap = new Map<string, string>();
+      for (const entry of systemConfig.projects) {
+        if (Array.isArray(entry) && entry.length >= 2 && typeof entry[0] === "string") {
+          const [projectPath, projectConfig] = entry;
+          systemProjectMap.set(projectPath, JSON.stringify(projectConfig));
+        }
+      }
+      const dataProjects = data.projects as Array<[string, unknown]>;
+      const filtered = dataProjects.filter(([projectPath, projectConfig]) => {
+        const systemProjectConfigJson = systemProjectMap.get(projectPath);
+        if (systemProjectConfigJson === undefined) {
+          return true; // User-only project.
+        }
+
+        return JSON.stringify(projectConfig) !== systemProjectConfigJson;
+      });
+
+      if (filtered.length === 0) {
+        delete data.projects;
+      } else {
+        data.projects = filtered;
+      }
+    }
   }
 
   loadConfigOrDefault(): ProjectsConfig {