fix: resolve config file read/write mismatch in update endpoint

packages/opencode/src/config/config.ts

@@ -1347,10 +1347,39 @@ export namespace Config {
   }
 
   export async function update(config: Info) {
-    const filepath = path.join(Instance.directory, "config.json")
-    const existing = await loadFile(filepath)
-    await Filesystem.writeJson(filepath, mergeDeep(existing, config))
+    const filepath = projectConfigFile()
+    const before = await Filesystem.readText(filepath).catch((err: any) => {
+      if (err.code === "ENOENT") return "{}"
+      throw new JsonError({ path: filepath }, { cause: err })
+    })
+
+    const next = await (async () => {
+      if (!filepath.endsWith(".jsonc")) {
+        const existing = parseConfig(before, filepath)
+        const merged = mergeDeep(existing, config)
+        await Filesystem.writeJson(filepath, merged)
+        return merged
+      }
+
+      const updated = patchJsonc(before, config)
+      const merged = parseConfig(updated, filepath)
+      await Filesystem.write(filepath, updated)
+      return merged
+    })()
+
     await Instance.dispose()
+    return next
+  }
+
+  function projectConfigFile() {
+    const candidates = ["opencode.jsonc", "opencode.json"].map((file) =>
+      path.join(Instance.directory, file),
+    )
+    for (const file of candidates) {
+      if (existsSync(file)) return file
+    }
+    // Default to opencode.json (standard project config file name)
+    return path.join(Instance.directory, "opencode.json")
   }
 
   function globalConfigFile() {

packages/opencode/src/server/routes/config.ts

@@ -54,8 +54,8 @@ export const ConfigRoutes = lazy(() =>
       validator("json", Config.Info),
       async (c) => {
         const config = c.req.valid("json")
-        await Config.update(config)
-        return c.json(config)
+        const next = await Config.update(config)
+        return c.json(next)
       },
     )
     .get(

packages/opencode/test/config/config.test.ts

@@ -683,14 +683,51 @@ test("updates config and writes to file", async () => {
     directory: tmp.path,
     fn: async () => {
       const newConfig = { model: "updated/model" }
-      await Config.update(newConfig as any)
+      const result = await Config.update(newConfig as any)
 
-      const writtenConfig = await Filesystem.readJson(path.join(tmp.path, "config.json"))
+      // Should return merged config
+      expect(result.model).toBe("updated/model")
+
+      // Should write to opencode.json by default (not config.json)
+      const writtenConfig = await Filesystem.readJson(path.join(tmp.path, "opencode.json"))
       expect(writtenConfig.model).toBe("updated/model")
     },
   })
 })
 
+test("updates existing opencode.json instead of creating config.json", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      // Create an existing opencode.json file
+      await writeConfig(dir, {
+        $schema: "https://opencode.ai/config.json",
+        model: "original/model",
+        username: "testuser",
+      })
+    },
+  })
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const newConfig = { model: "updated/model" }
+      const result = await Config.update(newConfig as any)
+
+      // Should return merged config with both old and new fields
+      expect(result.model).toBe("updated/model")
+      expect(result.username).toBe("testuser")
+
+      // Should update existing opencode.json (not create config.json)
+      const writtenConfig = await Filesystem.readJson(path.join(tmp.path, "opencode.json"))
+      expect(writtenConfig.model).toBe("updated/model")
+      expect(writtenConfig.username).toBe("testuser") // Should preserve existing fields
+
+      // config.json should not be created
+      const configJsonExists = await Filesystem.exists(path.join(tmp.path, "config.json"))
+      expect(configJsonExists).toBe(false)
+    },
+  })
+})
+
 test("gets config directories", async () => {
   await using tmp = await tmpdir()
   await Instance.provide({