MCP settings wiped when multiple windows open — race in McpHub.getMcpSettingsFilePath() direct fs.writeFile

Summary

Opening multiple VS Code windows concurrently can wipe mcp_settings.json to a 122-byte stub {"mcpServers": {}}, losing all MCP server configurations. Root cause is a race in McpHub.getMcpSettingsFilePath() which uses direct fs.writeFile without advisory lock, bypassing the existing safeWriteJson utility.

Environment

• Extension: zoocodeorganization.zoo-code v3.80.0
• OS: Linux (generic)
• VS Code: multiple windows / workspaces open simultaneously

Steps to Reproduce

1. Have a populated mcp_settings.json at ~/.config/Code/User/globalStorage/zoocodeorganization.zoo-code/settings/mcp_settings.json (or equivalent globalStorage path) with several mcpServers entries.
2. Open 2+ VS Code windows at roughly the same time (e.g., code . in two workspaces, or restoring session with multiple windows).
3. Each window constructs McpHub, which calls getMcpSettingsFilePath() → ensureSettingsDirectoryExists() → fileExistsAtPath() → fs.writeFile if not exists.
4. Observe file truncated to 122 bytes.

Observed Behavior

• File mcp_settings.json becomes:

  {
    "mcpServers": {
  
    }
  }

  (122 bytes, pretty-printed empty stub)
• stat shows Birth == Modify == 07:54 (file recreated at that time), indicating overwrite rather than edit.
• FileSystemWatcher (watchMcpSettingsFile) silently accepts the stub as valid config and propagates empty server list to all windows via debounceConfigChange → updateServerConnections({}, "global").
• All MCPs disappear from UI; no error shown (empty object passes McpSettingsSchema validation).

Expected Behavior

• Concurrent initializations should not clobber existing config.
• File creation should be atomic and locked, preserving existing servers.

Root Cause

File: src/services/mcp/McpHub.ts:496-517 (getMcpSettingsFilePath())

const fileExists = await fileExistsAtPath(mcpSettingsFilePath)
if (!fileExists) {
  await fs.writeFile(
    mcpSettingsFilePath,
    `{
  "mcpServers": {

  }
}`,
  )
}

• Uses direct fs.writeFile without lock, while src/utils/safeWriteJson.ts:45 exists and is already used elsewhere in same file (lines 2073, 2158, 2367) for other config writes.
• safeWriteJson provides proper-lockfile advisory lock (stale 31s, 5 retries, exponential backoff), temp file + atomic rename, and backup/rollback. This path bypasses it.
• TOCTOU: two processes both see fileExists==false (or one checks while other is mid-write), second blind write wins and truncates.
• No merge guard: even if file was just created by another window with content, it is overwritten with empty stub.

Watcher: watchMcpSettingsFile() at McpHub.ts:519 debounces and calls handleConfigFileChange which does JSON.parse + McpSettingsSchema.safeParse — empty mcpServers is valid, so no error is surfaced.

Impact

• Data loss: All MCP server definitions wiped (API keys, commands, URLs, env). User must restore from backup.
• Silent: No error toast; user discovers only when MCPs missing.
• Reproducible: Race window is small but reliably hit when opening multiple windows on session restore or via CLI.

Proposed Fix

Replace direct write with safeWriteJson:

- await fs.writeFile(
-   mcpSettingsFilePath,
-   `{
-   "mcpServers": {
-
-   }
- }`,
- )
+ await safeWriteJson(mcpSettingsFilePath, { mcpServers: {} }, { prettyPrint: true })

• Import already exists: import { safeWriteJson } from "../../utils/safeWriteJson" at McpHub.ts:44.
• safeWriteJson handles lock, atomic write, dir creation.

Optional stronger guard (handles TOCTOU between fileExistsAtPath and lock):

await safeWriteJson(mcpSettingsFilePath, { mcpServers: {} }, {
  prettyPrint: true,
  merge: (existing, incoming) => {
    if (existing && typeof existing === "object" && "mcpServers" in existing) {
      const ex = existing as { mcpServers?: Record<string, unknown> }
      if (ex.mcpServers && Object.keys(ex.mcpServers).length > 0) return existing
    }
    return incoming
  }
})

This makes it atomic read-modify-write under lock.

Patch prepared against v3.80.0 tag; source-only (installed dist/extension.js is minified, not patched). Patch file available on request.

Workaround Until Fixed

• Open single window at a time, or stagger window opens by a few seconds.
• Keep manual backup: e.g., ~/Desktop/CODE/ZooMCPBakup/mcp_settings.json (or any versioned backup outside globalStorage).
• Restore via cp ~/Desktop/CODE/ZooMCPBakup/mcp_settings.json ~/.config/Code/User/globalStorage/zoocodeorganization.zoo-code/settings/mcp_settings.json and reload window.

Additional Context

• No duplicate found for mcp_settings.json race OR McpHub race OR mcp wipe (searched via gh issue list).
• File references: McpHub.ts:496, safeWriteJson.ts:45, GlobalFileNames.mcpSettings.
• Willing to submit PR with above patch.

Checklist

• Searched existing issues — no duplicate
• Anonymized paths (no personal info)
• Includes code refs and proposed fix