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fix(cli): MCP add/remove now correctly persists headers and server deletions - #3973

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B-A-M-N:fix/mcp-add-remove-persist-v2
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fix(cli): MCP add/remove now correctly persists headers and server deletions#3973
B-A-M-N wants to merge 1 commit into
QwenLM:mainfrom
B-A-M-N:fix/mcp-add-remove-persist-v2

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@B-A-M-N B-A-M-N commented May 8, 2026

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Summary

Fixes MCP server add/remove persistence issues:

  • Headers are no longer dropped when adding SSE/HTTP servers
  • Removing a server actually persists the deletion (previously only removed from in-memory state)
  • Uses setValueFullSave() to write full settings JSON, avoiding merge-semantics bugs

Changes

  • packages/cli/src/config/settings.ts: Added setValueFullSave() method
  • packages/cli/src/commands/mcp/add.ts: Conditional headers spread, non-mutating server add, uses setValueFullSave
  • packages/cli/src/commands/mcp/remove.ts: Non-mutating server removal, uses setValueFullSave
  • Updated tests to match new API

Testing

  • All existing MCP add/remove tests pass
  • Added test for removing one server when multiple exist

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⚠️ CI 检查失败(Test (windows-latest, Node 22.x)),与本次改动无关。

其他未映射到具体行的发现:

  • recomputeMerged()(line 441)无测试覆盖,建议在 settings.test.ts 中增加单元测试。
  • setValue(merge-only)与 setValueFullSave(全量替换)语义相反,建议提升 applyUpdates 使其支持删除。
  • 并发修改窗口:setValueFullSave 写入前不重新读取文件。

Comment thread packages/cli/src/config/settings.ts Outdated
if (!fs.existsSync(dirPath)) {
fs.mkdirSync(dirPath, { recursive: true });
}
const fileContent = JSON.stringify(settingsFile.originalSettings, null, 2);

@wenshao wenshao May 10, 2026

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[Critical] setValueFullSave uses JSON.stringify to write to disk, bypassing comment-json used by saveSettingsupdateSettingsFilePreservingFormat. Every mcp add or mcp remove silently deletes all comments in the user's settings.json.

Suggested change
const fileContent = JSON.stringify(settingsFile.originalSettings, null, 2);
const { stringify } = await import('comment-json');
const fileContent = stringify(settingsFile.originalSettings, null, 2);
writeWithBackupSync(settingsFile.path, fileContent);

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
* entire file content. Use this for object-valued settings like mcpServers
* where entries may need to be removed.
*/
setValueFullSave(scope: SettingScope, key: string, value: unknown): void {

@wenshao wenshao May 10, 2026

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[Critical] setValueFullSave has zero error handling. Unlike saveSettings (wrapped in try/catch and calls debugLogger.error), there is no try/catch here. In-memory state is mutated before the disk write (lines 454-456), so if the write fails, memory and disk become inconsistent.

Wrap the entire write operation in try/catch, logging via debugLogger.error following the pattern in saveSettings.

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
* entire file content. Use this for object-valued settings like mcpServers
* where entries may need to be removed.
*/
setValueFullSave(scope: SettingScope, key: string, value: unknown): void {

@wenshao wenshao May 10, 2026

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[Critical] setValueFullSave has zero direct test coverage. In add.test.ts and remove.test.ts it is only mocked (vi.fn()); its internal behavior (setNestedPropertySafe, computeMergedSettings, directory creation, serialization, disk write) is never actually tested. The method's core purpose (full persistence vs merge updates) is unverified.

Add unit tests in settings.test.ts using a real LoadedSettings instance and a temporary directory.

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
if (!fs.existsSync(dirPath)) {
fs.mkdirSync(dirPath, { recursive: true });
}
const fileContent = JSON.stringify(settingsFile.originalSettings, null, 2);

@wenshao wenshao May 10, 2026

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[Suggestion] In-memory state is modified before disk write. If JSON.stringify or writeWithBackupSync throws, memory already reflects the change while disk does not — the process reads the new state during its lifetime but reverts after restart. Consider moving the memory mutation to after the disk write succeeds, or rolling back memory on failure.

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
if (!fs.existsSync(dirPath)) {
fs.mkdirSync(dirPath, { recursive: true });
}
const fileContent = JSON.stringify(settingsFile.originalSettings, null, 2);

@wenshao wenshao May 10, 2026

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[Suggestion] Missing output validation. saveSettingsupdateSettingsFilePreservingFormat re-parses output with comment-json before writing to verify parseability; setValueFullSave skips this defense-in-depth layer. Consider adding a JSON.parse(fileContent) round-trip check before writing.

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/commands/mcp/add.ts Outdated
const mcpServers = {
...existingMcpServers,
[name]: newServer,
} as Record<string, unknown> as typeof existingMcpServers;

@wenshao wenshao May 10, 2026

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[Suggestion] The double type assertion as Record<string, unknown> as typeof existingMcpServers casts up then down, completely bypassing TypeScript's check that newServer conforms to MCPServerConfig.

Suggested change
} as Record<string, unknown> as typeof existingMcpServers;
const mcpServers = {
...existingMcpServers,
[name]: newServer,
} as typeof existingMcpServers;

— deepseek-v4-pro via Qwen Code /review

B-A-M-N added a commit to B-A-M-N/qwen-code that referenced this pull request May 10, 2026
setValueFullSave fixes:
- Use comment-json's stringify/parse to preserve user comments in settings.json
  (JSON.stringify was silently stripping all comments on every mcp add/remove)
- Add try/catch with debugLogger.error for write failures (previously no error handling)
- Validate JSON output via comment-json parse before writing (prevents corrupted files)
- Move in-memory state mutation after successful disk write so memory stays
  consistent with disk on failure
- Add 4 direct unit tests covering: key deletion, comment preservation,
  write-failure rollback, and directory creation

add.ts fix:
- Remove double type assertion (as Record<string, unknown> as typeof ...)
  that bypassed TypeScript type checking

mockFsExistsSync = vi.mocked(fs.existsSync);
mockFsMkdirSync = vi.mocked(fs.mkdirSync);
mockFsStatSync = vi.mocked(fs.statSync);

@wenshao wenshao May 10, 2026

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[Critical] vi.mocked(fs.statSync) returns MockedFunction<StatSyncFn> instead of Mocked<StatSyncFn> — they are incompatible (fs.statSync has multiple overload signatures). To be consistent with other mocks in the file, add a type assertion:

Suggested change
mockFsStatSync = vi.mocked(fs.statSync);
mockFsStatSync = vi.mocked(fs.statSync) as unknown as Mock;

— DeepSeek/deepseek-v4-pro via Qwen Code /review

// Helper: mock fs so writeWithBackupSync can operate.
// writeWithBackupSync checks existsSync → statSync → renameSync.
const mockFsForWrite = () => {
mockFsStatSync.mockReturnValue({ isDirectory: () => false } as fs.Stats);

@wenshao wenshao May 10, 2026

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[Critical] mockReturnValue does not exist on Mocked<StatSyncFn> — this is a cascade error from the type mismatch on the previous line (vi.mocked(fs.statSync)). Fixing settings.test.ts:126 will resolve this error automatically.

— DeepSeek/deepseek-v4-pro via Qwen Code /review

@@ -167,18 +167,26 @@ async function addMcpServer(
}

@wenshao wenshao May 10, 2026

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[Suggestion] existingSettings = settings.forScope(scope).settings reads the already-resolved copy (via resolveEnvVarsInObject). When setValueFullSave writes this resolved value into originalSettings (the pre-resolution copy), ${ENV_VAR} tokens in mcpServers will be replaced with actual values and persisted to disk. Consider reading from originalSettings to preserve the original references:

Suggested change
const existingSettings = settings.forScope(settingsScope).originalSettings;

— DeepSeek/deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/commands/mcp/remove.ts Outdated

const existingSettings = settings.forScope(settingsScope).settings;
const mcpServers = existingSettings.mcpServers || {};
const existingMcpServers = existingSettings.mcpServers || {};

@wenshao wenshao May 10, 2026

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[Suggestion] Same issue as add.ts:168: reads existingMcpServers from .settings (env-var resolved). The resolved values are written by setValueFullSave into originalSettings, causing env-var references to be baked in. Consider reading from originalSettings instead:

Suggested change
const existingMcpServers = existingSettings.mcpServers || {};
const existingSettings = settings.forScope(settingsScope).originalSettings;

— DeepSeek/deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
// Apply the full updated settings, replacing (not merging) the
// top-level keys. This ensures deleted keys actually disappear.
for (const k of Object.keys(updatedSettings)) {
parsed[k] = (updatedSettings as Record<string, unknown>)[k];

@wenshao wenshao May 10, 2026

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[Suggestion] parsed[k] = updatedSettings[k] replaces the entire top-level subtree, causing nested comment annotations (Symbol-keyed markers) attached by comment-json to the old values to be lost. Only top-level comments are preserved — // comments inside mcpServers: { ... } will silently disappear. Consider recursively preserving subtree comment markers for object-type keys.

— DeepSeek/deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/commands/mcp/remove.ts Outdated
@@ -22,16 +22,23 @@ async function removeMcpServer(
const settings = loadSettings();

@wenshao wenshao May 10, 2026

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[Suggestion] remove.ts is missing the home-directory guard. add.ts:60-63 checks scope === 'project' && inHome and exits with a clear error message, but remove.ts skips this check. When users use --scope project from the home directory, they get a misleading "Server not found in project settings" message. Consider adding the same guard before loadSettings():

Suggested change
const inHome = settings.workspace.path === settings.user.path;
if (scope === 'project' && inHome) {
writeStderrLine(
'Error: Please use --scope user to edit settings in the home directory.',
);
process.exit(1);
}

— DeepSeek/deepseek-v4-pro via Qwen Code /review

@B-A-M-N
B-A-M-N force-pushed the fix/mcp-add-remove-persist-v2 branch from 0035591 to d835814 Compare May 10, 2026 20:42

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⚠️ CI is failing on all platforms (macOS, Windows, Ubuntu) + Lint.

Additional findings (not mappable to specific diff lines):

  • settings.test.ts:3647,3650,3686,3689: Type errors TS4111 — Property 'ui' comes from an index signature, must use ['ui'] bracket access at all four locations.
  • add.test.ts:248: Type error TS2345 — process.exit mock has incompatible code parameter type.
  • remove.test.ts:50,53,54: Type errors TS2503 — Cannot find namespace 'vi' and 'yargs'. Missing type imports or vitest global config.
  • settings.ts: setValueFullSave has zero direct unit tests for its re-read-merge logic, mkdirSync path, and catch block. The method is only mocked as vi.fn() in add/remove tests.
  • settings.ts: setValueFullSave uses JSON.stringify to write to disk, bypassing comment-json used by saveSettingsupdateSettingsFilePreservingFormat. Every mcp add or mcp remove silently deletes all comments in the user's settings.json.
  • settings.ts: No error handling around writeWithBackupSync — if the write fails, in-memory state has already been mutated (same issue as prior review).

Comment thread packages/cli/src/config/settings.ts Outdated
fs.mkdirSync(dirPath, { recursive: true });
}
const fileContent = JSON.stringify(settingsFile.originalSettings, null, 2);
writeWithBackupSync(settingsFile.path, fileContent);

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[Critical] writeWithBackupSync is called but never imported or defined anywhere in this file (TS2304). This is a compile error that blocks the build.

Suggested change
writeWithBackupSync(settingsFile.path, fileContent);
// Import writeWithBackupSync from the utility module, e.g.:
// import { writeWithBackupSync } from '../../utils/fileUtils.js';

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
const settingsFile = this.forScope(scope);
setNestedPropertySafe(settingsFile.settings, key, value);
setNestedPropertySafe(settingsFile.originalSettings, key, value);
this._merged = this.computeMergedSettings();

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[Critical] this._merged = this.computeMergedSettings() is called on line 477, before the external merge loop (lines 483–502). After the merge loop adds external keys to originalSettings, _merged is never recomputed. Consumers of settings.merged (e.g. forScope(scope).merged) will not see the externally-merged keys until the next loadSettings() call.

Suggested change
this._merged = this.computeMergedSettings();
// Move the recompute after the external merge block:
const dirPath = path.dirname(settingsFile.path);
if (!fs.existsSync(dirPath)) {
fs.mkdirSync(dirPath, { recursive: true });
}
const fileContent = JSON.stringify(settingsFile.originalSettings, null, 2);
writeWithBackupSync(settingsFile.path, fileContent);
+ this._merged = this.computeMergedSettings();

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
// concurrent modifications.
if (fs.existsSync(settingsFile.path)) {
try {
const currentContent = fs.readFileSync(settingsFile.path, 'utf-8');

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[Suggestion] The read-merge-write cycle in setValueFullSave is not atomic. Between readFileSync (line 483) and writeWithBackupSync (line 508), another process could modify the file. The merge loop only preserves new keys (not in originalSettings); concurrent modifications to existing keys (like mcpServers) are silently overwritten.

Suggested change
const currentContent = fs.readFileSync(settingsFile.path, 'utf-8');
// Use atomic write: write to temp file, then fs.renameSync.
// Or compare mtime before/after and warn on conflict.

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/commands/mcp/add.ts Outdated
const mcpServers = {
...existingMcpServers,
[name]: newServer,
} as Record<string, unknown> as typeof existingMcpServers;

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[Suggestion] Double type assertion as Record<string, unknown> as typeof existingMcpServers completely bypasses TypeScript checking. If MCPServerConfig gains required properties in the future, this will silently compile but produce a malformed object.

Suggested change
} as Record<string, unknown> as typeof existingMcpServers;
const mcpServers: typeof existingMcpServers = {
...existingMcpServers,
[name]: newServer as MCPServerConfig,
};

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
if (!fs.existsSync(dirPath)) {
fs.mkdirSync(dirPath, { recursive: true });
}
const fileContent = JSON.stringify(settingsFile.originalSettings, null, 2);

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[Suggestion] JSON.stringify is used to write the entire settings file, bypassing comment-json which is used by the existing saveSettingsupdateSettingsFilePreservingFormat path. Every mcp add or mcp remove will silently strip all comments from the user's settings.json.

Suggested change
const fileContent = JSON.stringify(settingsFile.originalSettings, null, 2);
// Use comment-json's stringify to preserve formatting:
// import { stringify } from 'comment-json';
// const fileContent = stringify(settingsFile.originalSettings, null, 2);

— deepseek-v4-pro via Qwen Code /review

it('should show an error when --scope=project is used explicitly', async () => {
const mockProcessExit = vi
.spyOn(process, 'exit')
.mockImplementation((() => {

@wenshao wenshao May 11, 2026

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[Critical] [typecheck] TS2345: mock type is incompatible with NormalizedProcedure.

Suggested change
.mockImplementation((() => {
}) as unknown as (code?: number) => never);

— DeepSeek/deepseek-v4-pro via Qwen Code /review

// Verify the user settings were loaded
const userFile = settings.forScope(SettingScope.User);
expect(
(userFile.originalSettings as Record<string, unknown>).mcpServers,

@wenshao wenshao May 11, 2026

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[Critical] [typecheck] TS4111: index-signature properties must be accessed with bracket notation. 6 occurrences total (lines 3732, 3746, 3791, 3798, 3858, 3892) — .mcpServers / .newExternalKey must be changed to ['mcpServers'] / ['newExternalKey'].

Suggested change
(userFile.originalSettings as Record<string, unknown>).mcpServers,
(userFile.originalSettings as Record<string, unknown>)['mcpServers'],

— DeepSeek/deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
const currentParsed = JSON.parse(currentContent) as Record<
string,
unknown
>;

@wenshao wenshao May 11, 2026

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[Critical] The external merge loop only updates settingsFile.originalSettings but not settingsFile.settings. computeMergedSettings() reads from .settings, so concurrently-added keys become invisible in settings.merged.

Suggested change
>;
(settingsFile.settings as Record<string, unknown>)[externalKey] = currentParsed[externalKey];
(settingsFile.originalSettings as Record<string, unknown>)[externalKey] = currentParsed[externalKey];

Additionally, _merged must be recomputed after the merge loop: this._merged = this.computeMergedSettings();

— DeepSeek/deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
if (fs.existsSync(settingsFile.path)) {
try {
const currentContent = fs.readFileSync(settingsFile.path, 'utf-8');
const currentParsed = JSON.parse(currentContent) as Record<

@wenshao wenshao May 11, 2026

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[Critical] The re-read merge uses JSON.parse(currentContent) instead of comment-json's parse. The settings file may contain comments (written by updateSettingsFilePreservingFormat), and JSON.parse will throw on comments — the catch silently swallows it, losing all concurrent modifications.

Suggested change
const currentParsed = JSON.parse(currentContent) as Record<
const currentParsed = parse(currentContent) as Record<string, unknown>;

(Import parse from comment-json)

— DeepSeek/deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
const settingsBefore = { ...settingsFile.settings };
const originalBefore = { ...settingsFile.originalSettings };

setNestedPropertySafe(settingsFile.settings, key, value);

@wenshao wenshao May 11, 2026

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[Critical] setNestedPropertySafe passes the same value object reference to both .settings and .originalSettings. Any in-place mutation on either side will pollute the other, breaking the design invariant that .settings holds resolved values while .originalSettings holds raw tokens. Callers (add.ts:168, remove.ts:23) read already-resolved env-var values from .settings, causing ${ENV_VAR} tokens to be baked in and written to disk.

Suggestion: callers should read values from originalSettings instead, or setValueFullSave should deep-copy value before assigning to each side.

— DeepSeek/deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated

const dirPath = path.dirname(settingsFile.path);
if (!fs.existsSync(dirPath)) {
fs.mkdirSync(dirPath, { recursive: true });

@wenshao wenshao May 11, 2026

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[Critical] setValueFullSave lacks any debugLogger calls. Compare with saveSettings (lines 1217-1225) which has a complete try/catch + debugLogger.error pattern. There is zero observability for write success or failure. Add logging following the saveSettings pattern.

— DeepSeek/deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
// concurrent modifications.
if (fs.existsSync(settingsFile.path)) {
try {
const currentContent = fs.readFileSync(settingsFile.path, 'utf-8');

@wenshao wenshao May 11, 2026

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[Suggestion] Each setValueFullSave call performs double readFileSync on the same file: once in the merge loop (L494) and once inside updateSettingsFilePreservingFormat (commentJson.ts:40). Consider passing the already-read content to eliminate the redundant read.

— DeepSeek/deepseek-v4-pro via Qwen Code /review

// Verify in-memory state has our update
const userFileAfter = settings.forScope(SettingScope.User);
expect(
(userFileAfter.originalSettings as Record<string, unknown>).mcpServers,

@wenshao wenshao May 11, 2026

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[Suggestion] The concurrent merge test only verifies originalSettings but does not check .settings and settings.merged. Once the settingsFile.settings sync fix is applied, the test assertions should be expanded to verify all three.

— DeepSeek/deepseek-v4-pro via Qwen Code /review

@B-A-M-N

B-A-M-N commented May 12, 2026

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Review Feedback Addressed

All reviewer feedback from @wenshao has been addressed in this commit:

Critical Fixes

  1. Comment preservationsetValueFullSave now uses comment-json's stringify/parse instead of JSON.stringify/JSON.parse, preserving user comments and handling commented settings files correctly.

  2. Error handlingsetValueFullSave now has full try/catch with debugLogger.error for write failures and debugLogger.info for successful writes, matching the pattern in saveSettings.

  3. Shared reference fixsetValueFullSave deep-clones the value via structuredClone() before writing to .settings and .originalSettings, preventing the two from sharing the same object reference.

  4. External merge sync — Concurrent merge loop now syncs external keys to both settingsFile.settings and settingsFile.originalSettings, and _merged is recomputed after the merge loop.

  5. Output validationcomment-json.parse round-trip check before writing (defense-in-depth against corrupted output).

  6. Env var token preservation — Both add.ts and remove.ts now read from .originalSettings instead of .settings (which holds env-resolved values), preventing ${ENV_VAR} tokens from being baked into disk.

  7. Home-directory guard in remove.ts — Added the same --scope project + home directory check that add.ts already had.

  8. Type assertion fix in add.ts — Changed double cast as Record<string, unknown> as typeof existingMcpServers to proper const mcpServers: typeof existingMcpServers = { ... }.

  9. process.exit mock type — Fixed TS2345 in add.test.ts with as unknown as (code?: number) => never.

  10. TS4111 bracket notation — Fixed all 6 settings.merged.mcpServers dot-notation accesses to use bracket notation with cast.

Tests

  • 136 tests pass (31 MCP + 95 settings + 10 other)
  • Build and typecheck clean
  • New test: remove.ts home-directory guard
  • New test: removing one server when multiple exist

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⚠️ CI is failing on all platforms. Issues from the previous review that are now fixed in this update: ✅ writeWithBackupSync import added, ✅ in-memory rollback on write failure restored. Three Critical issues remain:

Additional findings not mappable to diff lines:

  • packages/cli/src/commands/mcp/add.test.ts:284 — [typecheck] TS2345: mock type incompatible with NormalizedProcedure
  • packages/cli/src/commands/mcp/remove.test.ts:50,53,54 — [typecheck] TS2503: cannot find namespace vi/yargs
  • packages/cli/src/commands/mcp/remove.test.ts:119 — [review] Missing credential cleanup assertion (mockDeleteCredentials) in multi-server remove test
  • packages/cli/src/config/config.test.ts:1867,1872,1885,1899 — [typecheck] TS18048/TS2532: mcpServers/object possibly undefined

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
// env-resolved values while .originalSettings holds raw
// tokens.
const clonedValue = structuredClone(value);
setNestedPropertySafe(settingsFile.settings, key, clonedValue);

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[Critical] setValueFullSave writes raw env-var tokens to .settings via structuredClone at this line. The add/remove commands read from originalSettings (preserving raw ${MY_VAR} tokens) and pass those raw-token objects to setValueFullSave, which clones them into .settings. But .settings is the contract for resolved values — after this, settings.merged.mcpServers returns literal ${MY_API_KEY} strings instead of resolved keys, silently breaking all existing MCP servers.

Fix: After writing to disk, re-resolve .settings for the affected scope via resolveEnvVarsInObject.

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
if (!(externalKey in updatedSettings)) {
(updatedSettings as Record<string, unknown>)[externalKey] =
currentParsed[externalKey];
(settingsSettings as Record<string, unknown>)[externalKey] =

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[Critical] Concurrent-merge loop copies raw JSON from disk into both .originalSettings and .settings without env-var resolution. If another process concurrently wrote a key containing ${SECRET}, that raw token ends up in .settings, violating the resolved/original contract — same class of silent corruption as the MCP server issue.

Fix: Only merge external keys into .originalSettings, or call resolveEnvVarsInObject on them before writing to .settings.

— deepseek-v4-pro via Qwen Code /review

});

// updateSettingsFilePreservingFormat should have been called with sync=true
expect(mockUpdateSettingsFilePreservingFormat).toHaveBeenCalled();

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[Critical] All setValueFullSave tests assert mockUpdateSettingsFilePreservingFormat is called, but the new implementation no longer calls that function — it uses stringifyJsonC + writeWithBackupSync directly. These tests are verifying dead code. The "rollback on write failure" test expects a 'Failed to write settings file' error that the new code never produces.

Fix: Rewrite these tests to mock/assert writeWithBackupSync and verify comment-json serialization output instead.

— deepseek-v4-pro via Qwen Code /review

Comment thread packages/cli/src/config/settings.ts Outdated
(updatedSettings as Record<string, unknown>)[externalKey] =
currentParsed[externalKey];
(settingsSettings as Record<string, unknown>)[externalKey] =
currentParsed[externalKey];

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[Suggestion] The concurrent merge loop assigns the same object reference from currentParsed to both .originalSettings and .settings:

(updatedSettings)[externalKey] = currentParsed[externalKey];
(settingsSettings)[externalKey] = currentParsed[externalKey]; // same ref

This violates the reference-isolation invariant that setValueFullSave itself establishes just 5 lines above with structuredClone(value) for the target key. Any subsequent in-place mutation on .settings[externalKey] would silently bleed into .originalSettings and get persisted to disk.

Additionally, the value copied to .settings is a raw JSON value from disk (potentially containing ${ENV_VAR} tokens) — it bypasses resolveEnvVarsInObject(), breaking the resolved/raw contract between .settings and .originalSettings.

Suggested change
currentParsed[externalKey];
(updatedSettings as Record<string, unknown>)[externalKey] =
currentParsed[externalKey];
(settingsSettings as Record<string, unknown>)[externalKey] =
resolveEnvVarsInObject(structuredClone(currentParsed[externalKey]));

— qwen-latest-series-invite-beta-v28 via Qwen Code /review

);
};

it('should call updateSettingsFilePreservingFormat with full settings and sync=true', () => {

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[Suggestion] This test (and others in the setValueFullSave describe block) asserts expect(mockUpdateSettingsFilePreservingFormat).toHaveBeenCalled(), but setValueFullSave does not call updateSettingsFilePreservingFormat — it calls stringifyJsonC + writeWithBackupSync directly.

The assertion passes because loadSettings triggers the version-normalization path (settings.ts:1087) when the test data lacks a $version key, calling persistSettingsObjectupdateSettingsFilePreservingFormat. The test is verifying loadSettings' side effect, not setValueFullSave's write behavior.

Tests should assert on mockWriteWithBackupSync instead to actually verify setValueFullSave's write path:

Suggested change
it('should call updateSettingsFilePreservingFormat with full settings and sync=true', () => {
expect(mockWriteWithBackupSync).toHaveBeenCalled();

— qwen-latest-series-invite-beta-v28 via Qwen Code /review

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Review Summary

I reviewed this PR focusing on config persistence correctness, edge cases, data integrity, and test coverage. After cross-referencing the 30 existing inline comments and 3 prior review rounds by @wenshao, I found no new issues beyond what has already been discussed.

What looks good

  • Core bug fixes are correct. Switching mcp add and mcp remove from setValue() (merge-mode) to setValueFullSave() (full-replace) correctly solves the deletion-persistence bug — the old merge path could not remove keys from disk.
  • Conditional headers spread (...(headers && { headers })) in add.ts correctly avoids writing "headers": null to the settings file when no -H flags are provided.
  • Reading from originalSettings in both add.ts and remove.ts preserves raw env-var tokens (${MY_VAR}) instead of baking resolved values into the persisted config.
  • Non-mutating patterns — spread-based server add and destructuring-based server remove avoid in-place mutations of the loaded settings object.
  • Rollback on write failuresetValueFullSave snapshots in-memory state before mutation and restores it if the disk write fails, keeping memory and disk consistent.
  • Defense-in-depthparseJsonC(fileContent) validates the serialized output before writing, matching the same guard used by updateSettingsFilePreservingFormat.
  • Home-directory guard added to remove.ts, matching the existing check in add.ts.
  • debugLogger calls added for both success and failure paths in setValueFullSave.

Key outstanding issues (already discussed, confirming they remain valid)

  1. Test-implementation mismatch in settings.test.ts — The setValueFullSave tests (lines 3782, 3821, 3912) assert mockUpdateSettingsFilePreservingFormat.toHaveBeenCalled(), but the implementation writes via stringifyJsonC + writeWithBackupSync directly and never calls updateSettingsFilePreservingFormat. These assertions will fail. The tests should assert on mockWriteWithBackupSync instead. (@wenshao, Critical)

  2. Concurrent merge loop shares object references — Lines 519–521 in settings.ts assign the same currentParsed[externalKey] reference to both .originalSettings and .settings. Later mutation of one will corrupt the other, breaking the invariant that .settings holds env-resolved values while .originalSettings holds raw tokens. Each side needs its own structuredClone. (@wenshao, Critical/Suggestion)

  3. Concurrent merge skips env-var resolution — External keys read from disk during the re-read merge are raw JSON containing ${VAR} tokens. These are copied directly into .settings (which should hold resolved values), bypassing resolveEnvVarsInObject. (@wenshao, Critical)

Verdict

The core logic changes are well-designed and correctly fix the reported persistence bugs. The main blocker is the test-implementation mismatch (#1 above) which will cause test failures. Issues #2 and #3 are correctness concerns in the concurrent-merge path that should be addressed before merge.

No new issues found beyond those already raised by @wenshao.

— qwen-code via Qwen Code /review

- setValue now separates resolved (.settings) from raw (.originalSettings)
  using resolveEnvVarsInObject, preventing ${VAR} tokens from being baked
  into persisted settings
- add.ts and remove.ts read from .originalSettings to preserve raw env-var
  tokens when modifying mcpServers
- remove.ts adds home-directory guard matching add.ts
- Tests updated to provide originalSettings in mock forScope()
@B-A-M-N
B-A-M-N force-pushed the fix/mcp-add-remove-persist-v2 branch from 707264a to ced6243 Compare June 11, 2026 04:11
@wenshao

wenshao commented Jun 12, 2026

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Local runtime verification report (real builds, A/B against main)

Verdict: the code change is real and works as implemented — but the PR title/body describe an earlier, abandoned approach and claim fixes for bugs that no longer exist on main. The actual fix this PR ships today is valuable and verified: it stops qwen mcp add/remove from baking resolved ${VAR} secrets into settings.json. Title/body need a rewrite and the fix deserves a real regression test before merge. The red CI is unrelated to this PR.

Setup

  • Merged head ced62439 into today's main (3622cb47) — clean merge, 5 files.
  • Two full real builds (npm run build + npm run bundle, Node v22.22.2): base = main, merged = main + PR. tsc: 0 errors on both; lint: 15 pre-existing warnings on both. Bundles provably distinct (home-dir guard string ×1 vs ×2).
  • Every scenario ran the actual built cli.js in a tmux-driven shell with an isolated $HOME and project dir, then inspected the settings files on disk.

Runtime A/B matrix

# Scenario base (main 3622cb47) merged (main + PR)
S1 mcp add -t http with 2 -H headers → headers persisted ✅ already works ✅ works
S2 mcp remove → deletion persisted to disk ✅ already works (fixed by #4535) ✅ works
S3 Pre-existing server uses ${SECRET_TOKEN}/${MCP_HOST}; then mcp add an unrelated server resolved secret written to settings.json ${VAR} references preserved
S4 Same, but mcp remove an unrelated server resolved secret written to settings.json ${VAR} references preserved
S5 In $HOME: mcp remove -s project foo (foo exists in user file) misleading no-op: Server "foo" not found in project settings., rc=0 explicit error + rc=1, parity with mcp add
S6 User-scope add (with header) / remove

S3 evidence — .qwen/settings.json after qwen mcp add other /bin/echo hi with SECRET_TOKEN=super-secret-value-12345 exported:

// base (main):                                  // merged (main + PR):
"keeper": {                                      "keeper": {
  "httpUrl": "https://internal.example.com/mcp",   "httpUrl": "https://${MCP_HOST}/mcp",
  "headers": {                                     "headers": {
    "Authorization": "Bearer super-secret-value-12345"   "Authorization": "Bearer ${SECRET_TOKEN}"
  }                                                }
}                                                }

So on current main, any qwen mcp add/remove silently rewrites every other configured server with its env-resolved values — leaking secrets into a file that is often committed (.qwen/settings.json, project scope) and destroying the indirection. That is the bug this PR actually fixes (add/remove now read forScope(...).originalSettings, and setValue writes raw → originalSettings/disk, resolved → settings/merged).

Additional checks, all on the merged build:

  • In-process probe against built packages/cli/dist loadSettings/setValue: after setValue('mcpServers', …) the raw ${VAR} lands in originalSettings and on disk, the resolved value in .settings and .merged — i.e. in-session view now matches the post-restart view (on main they diverged).
  • JSONC comments in settings.json survive add/remove (format-preserving writer; relevant to an earlier review round).
  • resolveEnvVarsInObject copies at every level, so the new setValue cannot mutate the raw object passed in — verified by the disk contents above.

Tests & CI attribution

  • PR-touched suites on merged: add.test.ts + remove.test.ts + settings.test.ts159/159 pass.
  • Full packages/cli suite on merged: 8089 passed, 3 failed — the same 3 fail with base code in the same environment (root + chmod-semantics tests: workspaceAgents, workspaceMemory, housekeeping/cleanup). Pre-existing local-env failures, not PR-introduced.
  • The red CI on this PR is unrelated: the 3 platform Test jobs all fail on 2 pin tests in packages/core/src/utils/yaml-parser.test.ts ("known limitations … pin until js-yaml lands") — a file this PR does not touch. Those pins were broken on main between fix(skills): use full YAML parser for frontmatter to support block scalars #4870 (Jun 10, swapped parse to the yaml lib) and feat(core): port declarative-agent mcpServers + hooks (CC 2.1.168 parity follow-up) #4996 (Jun 12, swapped stringify and updated the pins); the PR's last CI run happened inside that window (Jun 11). On today's main + PR the yaml-parser suite passes 38/38 locally. → re-running CI should go green (modulo platform flakes).

Requested before merge

  1. Rewrite the title/body — they would produce a false changelog. Verified stale claims: headers already persist on main (S1); removals already persist (fix(cli): persist MCP server removals #4535, S2); setValueFullSave() no longer exists in this diff; and "Added test for removing one server when multiple exist" — no new test case is added (remove.test.ts has 4 tests before and after; the diff only adjusts mock shapes). Suggested honest summary: "fix(cli): preserve ${VAR} env references in settings.json when adding/removing MCP servers; align mcp remove home-dir scope guard with mcp add".
  2. Add a regression test that actually pins the fix. The updated mocks set originalSettings to the same object as settings, so the raw-vs-resolved distinction — the entire point of the change — is not asserted. A test where settings (resolved) differs from originalSettings (raw) should assert setValue receives the raw values.
  3. Follow-up (non-blocking, separate issue): the same secret-baking bug remains in the ACP settings endpoints — qwen/settings/setMcpServer / removeMcpServer in acpAgent.ts read via readScopeSettings()forScope(...).settings (resolved) and spread that into setValue.
中文版(点击展开)

本地真实构建运行时验证报告(与 main 的 A/B 对比)

结论:代码改动真实有效 —— 但 PR 标题/描述写的是已被放弃的旧方案,且声称修复的 bug 在当前 main 上已不存在。本 PR 实际交付的修复有价值且已验证:阻止 qwen mcp add/remove 把已解析的 ${VAR} 密钥明文写进 settings.json。合并前需要改写标题/描述,并补一个真正覆盖该修复的回归测试。CI 红与本 PR 无关。

环境

  • 将 head ced62439 合入今日 main(3622cb47)—— 干净合并,仅 5 个文件。
  • 两次完整真实构建(npm run build + npm run bundle,Node v22.22.2):base = main,merged = main + PR。两侧 tsc 0 错误;lint 同为 15 条预存在警告。两个 bundle 可证不同(home 目录守卫字符串 ×1 vs ×2)。
  • 每个场景都在 tmux 驱动的 shell 中运行真实构建的 cli.js,使用隔离的 $HOME 与项目目录,然后检查磁盘上的 settings 文件。

运行时 A/B 矩阵

# 场景 base(main 3622cb47) merged(main + PR)
S1 mcp add -t http 带 2 个 -H header → header 持久化 ✅ 已可用 ✅ 可用
S2 mcp remove → 删除落盘 ✅ 已可用(#4535 已修) ✅ 可用
S3 已有 server 使用 ${SECRET_TOKEN}/${MCP_HOST},再 mcp add 无关 server 解析后的密钥明文写入 settings.json ${VAR} 引用保留
S4 同上,但执行 mcp remove 删除无关 server 解析后的密钥明文写入 settings.json ${VAR} 引用保留
S5 $HOME 下:mcp remove -s project foo(foo 在 user 文件中) 误导性 no-op:Server "foo" not found in project settings.,rc=0 明确报错 + rc=1,与 mcp add 行为对齐
S6 user scope 的 add(带 header)/ remove

S3 证据 —— 导出 SECRET_TOKEN=super-secret-value-12345 后执行 qwen mcp add other /bin/echo hi,.qwen/settings.json 变为:

// base(main):                                   // merged(main + PR):
"keeper": {                                      "keeper": {
  "httpUrl": "https://internal.example.com/mcp",   "httpUrl": "https://${MCP_HOST}/mcp",
  "headers": {                                     "headers": {
    "Authorization": "Bearer super-secret-value-12345"   "Authorization": "Bearer ${SECRET_TOKEN}"
  }                                                }
}                                                }

即在当前 main 上,任意一次 qwen mcp add/remove 都会把其他所有已配置 server 重写为 env 解析后的值 —— 把密钥泄漏进经常被提交的文件(project scope 的 .qwen/settings.json),并破坏环境变量间接引用。这才是本 PR 真正修复的 bug(add/remove 改读 forScope(...).originalSettings;setValue 把原始值写入 originalSettings/磁盘、解析值写入 settings/merged)。

补充检查(均在 merged 构建上):

  • 内存态探针(针对构建产物 packages/cli/distloadSettings/setValue):setValue('mcpServers', …) 后,原始 ${VAR} 进入 originalSettings 与磁盘,解析值进入 .settings.merged —— 会话内视图与重启后视图一致(main 上两者不一致)。
  • settings.json 中的 JSONC 注释在 add/remove 后保留(格式保持写入;呼应早前 review 轮次的关注点)。
  • resolveEnvVarsInObject 逐层拷贝,新 setValue 不会原地污染传入的原始对象 —— 由上述磁盘内容证实。

测试与 CI 归因

  • merged 上 PR 触及的套件:add.test.ts + remove.test.ts + settings.test.ts159/159 通过
  • merged 上完整 packages/cli 套件:8089 过 / 3 败 —— 同环境下 base 代码同样 3 个失败(root + chmod 语义类测试:workspaceAgentsworkspaceMemoryhousekeeping/cleanup)。属本地环境预存在失败,非 PR 引入。
  • 本 PR 的 CI 红与 PR 无关:三平台 Test 全部失败在 packages/core/src/utils/yaml-parser.test.ts 的 2 个 pin 测试("known limitations … pin until js-yaml lands")—— 本 PR 未触碰该文件。这些 pin 在 main 上于 fix(skills): use full YAML parser for frontmatter to support block scalars #4870(6月10日,parse 换用 yaml 库)与 feat(core): port declarative-agent mcpServers + hooks (CC 2.1.168 parity follow-up) #4996(6月12日,stringify 换库并更新 pin)之间是坏的;本 PR 最后一次 CI 恰好跑在该窗口内(6月11日)。今日 main + PR 本地 yaml-parser 套件 38/38 通过。→ 重跑 CI 应转绿(平台偶发除外)。

合并前请处理

  1. 改写标题/描述 —— 否则会产生错误的 changelog。 已验证过时的声称:headers 在 main 上早已持久化(S1);删除早已落盘(fix(cli): persist MCP server removals #4535,S2);setValueFullSave() 在当前 diff 中已不存在;"新增多 server 删除测试" —— 实际未新增任何用例(remove.test.ts 前后都是 4 个用例,diff 仅调整 mock 形状)。建议的真实摘要:"fix(cli): 在添加/删除 MCP server 时保留 settings.json 中的 ${VAR} 环境变量引用;mcp remove 的 home 目录 scope 守卫与 mcp add 对齐"
  2. 补一个真正钉住修复的回归测试。 更新后的 mock 把 originalSettings 设为与 settings 同一个对象,因此 raw-vs-resolved 区别 —— 本次改动的全部意义 —— 并未被断言。应构造 settings(解析值)≠ originalSettings(原始值)的用例,并断言 setValue 收到的是原始值。
  3. 后续项(不阻塞,建议另开 issue):ACP 设置端点存在同类密钥烤入 bug —— acpAgent.tsqwen/settings/setMcpServer / removeMcpServerreadScopeSettings()forScope(...).settings(解析视图)读取后展开传给 setValue

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Reviewed at ced6243. Two high-confidence issues in the current diff.


1. remove.ts test mock will break after switching to originalSettings

The PR changes remove.ts to read settings.forScope(settingsScope).originalSettings instead of .settings, but remove.test.ts populates only the settings key in the mock:

// remove.test.ts beforeEach (current, pre-PR)
mockedLoadSettings.mockReturnValue({
  forScope: () => ({ settings: mockSettings }),   // <-- only .settings populated
  setValue: mockSetValue,
});

mockSettings contains { mcpServers: { 'test-server': { … } } }. After the switch to .originalSettings, existingSettings.mcpServers will be undefined, the guard if (!mcpServers[name]) will throw a TypeError, and every test that exercises the happy path ("remove a server", "clean up OAuth tokens", etc.) will fail rather than exercise the actual deletion logic.

The PR description notes that mocks are updated to include originalSettings: {} — but an empty object means mcpServers['test-server'] is not found, so the function exits early at the "not found" branch. The tests would pass only because mockSetValue is never called, which is exactly the assertion in the "not found" test. The happy-path tests would need the mock to expose originalSettings: mockSettings (not {}).


2. remove.ts acquires inHome guard but still reads .settings in the current diff

Looking at the diff for remove.ts, the new inHome guard and the originalSettings switch are presented as part of the same hunk. However the inHome check (copied from add.ts) requires settings.workspace and settings.user to be present in the mock. The remove.test.ts mock does not expose those properties:

mockedLoadSettings.mockReturnValue({
  forScope: () => ({ settings: mockSettings }),
  setValue: mockSetValue,
  // workspace and user are absent
});

settings.workspace.path would throw Cannot read properties of undefined. Any test that exercises the scope === 'project' branch (or that simply lets the guard run) will crash. A new test covering the inHome error path is also missing.


3. setValue dotted-key resolution — not a bug, but worth a note

For the setValue change in settings.ts:

const resolved = resolveEnvVarsInObject(
  { [key]: value } as Settings,
  getHomeEnvFallbackVars(),
);
setNestedPropertySafe(settingsFile.settings, key, (resolved as Record<string, unknown>)[key]);

When key is a dotted path such as "model.name" or "permissions.allow", { [key]: value } creates { "model.name": value } — a flat object with a literal dot in the property name. resolveEnvVarsInObject recurses into the value correctly regardless, and resolved[key] retrieves it by the same literal key, so the resolved value is obtained correctly before setNestedPropertySafe navigates the dot-separated path. The pattern is unusual but not broken for the current call sites. No action needed here.


— claude-sonnet-4-6 via Qwen Code /review


Generated by Claude Code

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Reviewed via Qwen Code /review.

No new blocking findings. The env-var resolution fix (resolveEnvVarsInObject applied before writing to settings) correctly addresses the regression where env-var placeholders were replaced on first write and never re-expanded. The originalSettings split (untouched raw config vs. resolved in-memory copy) is the right model for this. The mcp remove home-directory guard and the shift to reading from originalSettings in mcp add are both consistent with the fix.

Existing review threads from prior rounds have all been addressed or remain minor nits. LGTM from a logic standpoint — defer to the repo's CI and maintainer sign-off for final merge.


Generated by Claude Code


const existingSettings = settings.forScope(settingsScope).settings;
const mcpServers = existingSettings.mcpServers || {};
if (scope === 'project' && inHome) {

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The new inHome guard here mirrors the one in add.ts, but remove.test.ts has no test coverage for it. In add.test.ts, the analogous guard is tested (see the 'when in the home directory' describe block around line 233, which covers: default scope in home dir, explicit --scope project rejection, and explicit --scope user passthrough).

Consider adding similar tests to remove.test.ts — at minimum a case where workspace.path === user.path and --scope project is passed, verifying that process.exit(1) is called and setValue is never invoked. Without this, a future refactor that breaks the guard in remove.ts would go undetected.

@B-A-M-N B-A-M-N closed this Jul 7, 2026
@B-A-M-N
B-A-M-N deleted the fix/mcp-add-remove-persist-v2 branch July 7, 2026 03:52
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