fix: resolve all test failures and Cubic review issues

- Fix unstable-agent-babysitter: add promptAsync to test mock
- Fix claude-code-mcp-loader: isolate tests from user home configs
- Fix npm-dist-tags: encode packageName for scoped packages
- Fix agent-builder: clone source to prevent shared object mutation
- Fix add-plugin-to-opencode-config: handle JSONC with leading comments
- Fix auth-plugins/add-provider-config: error on parse failures
- Fix bun-install: clear timeout on completion
- Fix git-diff-stats: include untracked files in diff summary

src/agents/agent-builder.ts

@@ -19,7 +19,7 @@ export function buildAgent(
   browserProvider?: BrowserAutomationProvider,
   disabledSkills?: Set<string>
 ): AgentConfig {
-  const base = isFactory(source) ? source(model) : source
+  const base = isFactory(source) ? source(model) : { ...source }
   const categoryConfigs: Record<string, CategoryConfig> = categories
     ? { ...DEFAULT_CATEGORIES, ...categories }
     : DEFAULT_CATEGORIES

src/cli/config-manager/add-plugin-to-opencode-config.ts

@@ -64,7 +64,7 @@ export async function addPluginToOpenCodeConfig(currentVersion: string): Promise
         const newContent = content.replace(pluginArrayRegex, `"plugin": [\n    ${formattedPlugins}\n  ]`)
         writeFileSync(path, newContent)
       } else {
-        const newContent = content.replace(/^(\s*\{)/, `$1\n  "plugin": ["${pluginEntry}"],`)
+        const newContent = content.replace(/(\{)/, `$1\n  "plugin": ["${pluginEntry}"],`)
         writeFileSync(path, newContent)
       }
     } else {

src/cli/config-manager/add-provider-config.ts

@@ -25,10 +25,13 @@ export function addProviderConfig(config: InstallConfig): ConfigMergeResult {
     if (format !== "none") {
       const parseResult = parseOpenCodeConfigFileWithError(path)
       if (parseResult.error && !parseResult.config) {
-        existingConfig = {}
+        return {
-      } else {
+          success: false,
-        existingConfig = parseResult.config
+          configPath: path,
+          error: `Failed to parse config file: ${parseResult.error}`,
+        }
       }
+      existingConfig = parseResult.config
     }
 
     const newConfig = { ...(existingConfig ?? {}) }

src/cli/config-manager/auth-plugins.ts

@@ -35,10 +35,13 @@ export async function addAuthPlugins(config: InstallConfig): Promise<ConfigMerge
     if (format !== "none") {
       const parseResult = parseOpenCodeConfigFileWithError(path)
       if (parseResult.error && !parseResult.config) {
-        existingConfig = {}
+        return {
-      } else {
+          success: false,
-        existingConfig = parseResult.config
+          configPath: path,
+          error: `Failed to parse config file: ${parseResult.error}`,
+        }
       }
+      existingConfig = parseResult.config
     }
 
     const plugins: string[] = existingConfig?.plugin ?? []

src/cli/config-manager/bun-install.ts

@@ -22,11 +22,13 @@ export async function runBunInstallWithDetails(): Promise<BunInstallResult> {
       stderr: "pipe",
     })
 
-    const timeoutPromise = new Promise<"timeout">((resolve) =>
+    let timeoutId: ReturnType<typeof setTimeout>
-      setTimeout(() => resolve("timeout"), BUN_INSTALL_TIMEOUT_MS)
+    const timeoutPromise = new Promise<"timeout">((resolve) => {
-    )
+      timeoutId = setTimeout(() => resolve("timeout"), BUN_INSTALL_TIMEOUT_MS)
+    })
     const exitPromise = proc.exited.then(() => "completed" as const)
     const result = await Promise.race([exitPromise, timeoutPromise])
+    clearTimeout(timeoutId!)
 
     if (result === "timeout") {
       try {

src/cli/config-manager/npm-dist-tags.ts

@@ -9,7 +9,7 @@ const NPM_FETCH_TIMEOUT_MS = 5000
 
 export async function fetchNpmDistTags(packageName: string): Promise<NpmDistTags | null> {
   try {
-    const res = await fetch(`https://registry.npmjs.org/-/package/${packageName}/dist-tags`, {
+    const res = await fetch(`https://registry.npmjs.org/-/package/${encodeURIComponent(packageName)}/dist-tags`, {
       signal: AbortSignal.timeout(NPM_FETCH_TIMEOUT_MS),
     })
     if (!res.ok) return null

src/features/claude-code-mcp-loader/loader.test.ts

@@ -4,10 +4,19 @@ import { join } from "path"
 import { tmpdir } from "os"
 
 const TEST_DIR = join(tmpdir(), "mcp-loader-test-" + Date.now())
+const TEST_HOME = join(TEST_DIR, "home")
 
 describe("getSystemMcpServerNames", () => {
   beforeEach(() => {
     mkdirSync(TEST_DIR, { recursive: true })
+    mkdirSync(TEST_HOME, { recursive: true })
+    mock.module("os", () => ({
+      homedir: () => TEST_HOME,
+      tmpdir,
+    }))
+    mock.module("../../shared", () => ({
+      getClaudeConfigDir: () => join(TEST_HOME, ".claude"),
+    }))
   })
 
   afterEach(() => {
@@ -162,7 +171,7 @@ describe("getSystemMcpServerNames", () => {
 
     it("reads user-level MCP config from ~/.claude.json", async () => {
       // given
-      const userConfigPath = join(TEST_DIR, ".claude.json")
+      const userConfigPath = join(TEST_HOME, ".claude.json")
       const userMcpConfig = {
         mcpServers: {
           "user-server": {
@@ -171,53 +180,37 @@ describe("getSystemMcpServerNames", () => {
           },
         },
       }
+      writeFileSync(userConfigPath, JSON.stringify(userMcpConfig))
 
       const originalCwd = process.cwd()
       process.chdir(TEST_DIR)
 
       try {
-        mock.module("os", () => ({
+        // when
-          homedir: () => TEST_DIR,
-          tmpdir,
-        }))
-
-        writeFileSync(userConfigPath, JSON.stringify(userMcpConfig))
-
         const { getSystemMcpServerNames } = await import("./loader")
         const names = getSystemMcpServerNames()
 
+        // then
         expect(names.has("user-server")).toBe(true)
       } finally {
         process.chdir(originalCwd)
-        rmSync(userConfigPath, { force: true })
       }
     })
 
     it("reads both ~/.claude.json and ~/.claude/.mcp.json for user scope", async () => {
-      // given: simulate both user-level config files
+      // given
-      const userClaudeJson = join(TEST_DIR, ".claude.json")
+      const claudeDir = join(TEST_HOME, ".claude")
-      const claudeDir = join(TEST_DIR, ".claude")
-      const claudeDirMcpJson = join(claudeDir, ".mcp.json")
-
       mkdirSync(claudeDir, { recursive: true })
 
-      // ~/.claude.json has server-a
+      writeFileSync(join(TEST_HOME, ".claude.json"), JSON.stringify({
-      writeFileSync(userClaudeJson, JSON.stringify({
         mcpServers: {
-          "server-from-claude-json": {
+          "server-from-claude-json": { command: "npx", args: ["server-a"] },
-            command: "npx",
-            args: ["server-a"],
-          },
         },
       }))
 
-      // ~/.claude/.mcp.json has server-b (CLI-managed)
+      writeFileSync(join(claudeDir, ".mcp.json"), JSON.stringify({
-      writeFileSync(claudeDirMcpJson, JSON.stringify({
         mcpServers: {
-          "server-from-mcp-json": {
+          "server-from-mcp-json": { command: "npx", args: ["server-b"] },
-            command: "npx",
-            args: ["server-b"],
-          },
         },
       }))
 
@@ -225,20 +218,11 @@ describe("getSystemMcpServerNames", () => {
       process.chdir(TEST_DIR)
 
       try {
-        mock.module("os", () => ({
+        // when
-          homedir: () => TEST_DIR,
-          tmpdir,
-        }))
-
-        // Also mock getClaudeConfigDir to point to our test .claude dir
-        mock.module("../../shared", () => ({
-          getClaudeConfigDir: () => claudeDir,
-        }))
-
         const { getSystemMcpServerNames } = await import("./loader")
         const names = getSystemMcpServerNames()
 
-        // Both sources should be merged
+        // then
         expect(names.has("server-from-claude-json")).toBe(true)
         expect(names.has("server-from-mcp-json")).toBe(true)
       } finally {

src/hooks/atlas/git-diff-stats.ts

@@ -9,15 +9,6 @@ interface GitFileStat {
 
 export function getGitDiffStats(directory: string): GitFileStat[] {
   try {
-    const output = execSync("git diff --numstat HEAD", {
-      cwd: directory,
-      encoding: "utf-8",
-      timeout: 5000,
-      stdio: ["pipe", "pipe", "pipe"],
-    }).trim()
-
-    if (!output) return []
-
     const statusOutput = execSync("git status --porcelain", {
       cwd: directory,
       encoding: "utf-8",
@@ -25,12 +16,18 @@ export function getGitDiffStats(directory: string): GitFileStat[] {
       stdio: ["pipe", "pipe", "pipe"],
     }).trim()
 
+    if (!statusOutput) return []
+
     const statusMap = new Map<string, "modified" | "added" | "deleted">()
+    const untrackedFiles: string[] = []
     for (const line of statusOutput.split("\n")) {
       if (!line) continue
       const status = line.substring(0, 2).trim()
       const filePath = line.substring(3)
-      if (status === "A" || status === "??") {
+      if (status === "??") {
+        statusMap.set(filePath, "added")
+        untrackedFiles.push(filePath)
+      } else if (status === "A") {
         statusMap.set(filePath, "added")
       } else if (status === "D") {
         statusMap.set(filePath, "deleted")
@@ -39,21 +36,49 @@ export function getGitDiffStats(directory: string): GitFileStat[] {
       }
     }
 
+    const output = execSync("git diff --numstat HEAD", {
+      cwd: directory,
+      encoding: "utf-8",
+      timeout: 5000,
+      stdio: ["pipe", "pipe", "pipe"],
+    }).trim()
+
     const stats: GitFileStat[] = []
-    for (const line of output.split("\n")) {
+    const trackedPaths = new Set<string>()
-      const parts = line.split("\t")
-      if (parts.length < 3) continue
 
-      const [addedStr, removedStr, path] = parts
+    if (output) {
-      const added = addedStr === "-" ? 0 : parseInt(addedStr, 10)
+      for (const line of output.split("\n")) {
-      const removed = removedStr === "-" ? 0 : parseInt(removedStr, 10)
+        const parts = line.split("\t")
+        if (parts.length < 3) continue
 
-      stats.push({
+        const [addedStr, removedStr, path] = parts
-        path,
+        const added = addedStr === "-" ? 0 : parseInt(addedStr, 10)
-        added,
+        const removed = removedStr === "-" ? 0 : parseInt(removedStr, 10)
-        removed,
+        trackedPaths.add(path)
-        status: statusMap.get(path) ?? "modified",
+
-      })
+        stats.push({
+          path,
+          added,
+          removed,
+          status: statusMap.get(path) ?? "modified",
+        })
+      }
+    }
+
+    for (const filePath of untrackedFiles) {
+      if (trackedPaths.has(filePath)) continue
+      try {
+        const content = execSync(`wc -l < "${filePath}"`, {
+          cwd: directory,
+          encoding: "utf-8",
+          timeout: 3000,
+          stdio: ["pipe", "pipe", "pipe"],
+        }).trim()
+        const lineCount = parseInt(content, 10) || 0
+        stats.push({ path: filePath, added: lineCount, removed: 0, status: "added" })
+      } catch {
+        stats.push({ path: filePath, added: 0, removed: 0, status: "added" })
+      }
     }
 
     return stats

src/hooks/unstable-agent-babysitter/index.test.ts

@@ -21,6 +21,9 @@ function createMockPluginInput(options: {
         prompt: async (input: unknown) => {
           promptCalls.push({ input })
         },
+        promptAsync: async (input: unknown) => {
+          promptCalls.push({ input })
+        },
       },
     },
   }