claude_desktop_config.json being reset continuously

[davidcim]

Every time I start claude-desktop, or if I change mode in the Claude top bar (chat/cowork/code), the file ~/.config/Claude/claude_desktop_config.json gets reset to the same content:

{
  "preferences": {
    "localAgentModeTrustedFolders": [
      "/usr/lib/claude-desktop/node_modules/electron/dist/resources/app.asar"
    ],
    "coworkScheduledTasksEnabled": true,
    "ccdScheduledTasksEnabled": true,
    "sidebarMode": "task",
    "coworkWebSearchEnabled": false,
    "floatingAtollActive": true
  }
}

It's not a formatting problem — the file is rewritten even if no changes are made, or if I toggle a simple boolean value. Furthermore, I can see in the log when it occurs:

2026-04-14 20:36:12 [info] Config file written

My problem is that I can't add any MCP server. If I add one, claude-desktop --doctor detects it correctly, but the config file gets reset on startup and my configuration is discarded.

My configuration

$ lsb_release -d
Description:    Ubuntu 22.04.5 LTS

$ claude-desktop --doctor
Claude Desktop Diagnostics
================================

[PASS] Installed version: 1.2278.0-1.3.30
[PASS] Display server: X11 (DISPLAY=:0)
       Menu bar mode: auto (default, Alt toggles visibility)
[PASS] Electron: v41.2.0 (/usr/lib/claude-desktop/node_modules/electron/dist/electron)
[PASS] Chrome sandbox: permissions OK (/usr/lib/claude-desktop/node_modules/electron/dist/chrome-sandbox)
[PASS] SingletonLock: held by running process (PID 3520986)
[PASS] MCP config: valid JSON (/home/david/.config/Claude/claude_desktop_config.json)
       MCP servers configured: 1
[PASS] Node.js: v20.20.2
       Path: /home/david/.nvm/versions/node/v20.20.2/bin/node
[PASS] Desktop entry: /usr/share/applications/claude-desktop.desktop
[PASS] Disk space: 20668MB free

Cowork Mode
----------------
[PASS] bubblewrap: found
[PASS] KVM: accessible
[PASS] vsock: module loaded
       QEMU: not found
[PASS] socat: found
       virtiofsd: not found
       VM image: not downloaded yet
       Cowork isolation: bubblewrap (namespace sandbox)
[PASS] Cowork daemon: running (parent alive)
[PASS] Log file: 23KB (/home/david/.cache/claude-desktop-debian/launcher.log)

[github-actions]

I've traced this to two independent bugs in the upstream app code, both fixable with build.sh patches.

Root cause 1 — stale in-memory cache. The config reader function memoizes the parsed config on first access and never refreshes it unless an internal forceReload=true flag is set. Every config write serializes that cached object back to disk. So if you edit claude_desktop_config.json after startup to add MCP servers, the next internal preference change (mode switch, hardware accel toggle, anything) calls KQ(To()), which serializes the stale cached copy and overwrites your edits. All five write paths funnel through one function — it's a full JSON.stringify replacement every time, no partial writes.

Root cause 2 — addTrustedFolder swallows the app install path. When a code session starts without an open project, the renderer passes a fallback CWD derived from Ce.app.getAppPath(). On Debian this resolves to /usr/lib/claude-desktop/node_modules/electron/dist/resources/app.asar. The addTrustedFolder function has no validation — it accepts any path, including .asar archives and non-directories — and appends it to localAgentModeTrustedFolders, then triggers a full config write. That's why you see that specific path show up in your config.

Two patches in build.sh should fix this. The first adds an early-return guard in addTrustedFolder to reject paths that aren't real directories:

# After the log line — insert guard before the rest of the function body
if(n.endsWith(".asar")||!require("fs").existsSync(n)||!require("fs").statSync(n).isDirectory())return;

The second wraps the write inside KQ to re-read mcpServers from disk and merge them into the object before writing — so a user's manually added MCP servers survive any preference change. The anchor for both patches is stable: "LocalAgentModeSessions.addTrustedFolder: " and "Config file written" each appear exactly once in index.js.

Related: #400 is the same issue.

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