[BUG] Cowork MCP tools broken on Fedora 42 — config silently wiped, Chrome bridge fails, local MCPs invisible

Environment

• OS: Fedora 42 (Adams), kernel 6.19.10-100.fc42.x86_64
• Desktop: GNOME Shell 48.7, Wayland
• Claude Desktop: claude-desktop-1.1.9669-1.3.26.fc42.x86_64 (RPM repack)
• Claude Code: 2.1.91
• MCP servers configured: 16

Bugs (4 confirmed, all reproducible)

1. Config silently wiped (relates to #32345)

claude_desktop_config.json gets overwritten with a preferences-only stub (~5 lines), destroying all 16 MCP server definitions (143 lines). No warning, no backup.
Workaround: chmod 444 on config file + cron watchdog.

2. Claude in Chrome bridge fails in Cowork (relates to #27492)

tabs_context_mcp returns 'Chrome extension is not reachable' every time. Chrome is open, extension installed and signed in. Bridge-type MCP from Cowork VM to host never establishes.

3. Local MCP tools inconsistent in Cowork (relates to #20377, #42453)

• Some stdio MCPs work (filesystem, ruflo), others fail
• claude-code-peer tools all fail: 'output schema but did not return structured content'
• computer:// protocol links dont open on Linux
• Tool permissions dont persist across sessions (#24433)

4. Session state not syncing

Claude Code sessions dont share context with Cowork. .claude/ memory files exist but Cowork doesnt read them.

Steps to reproduce

1. Install Claude Desktop on Fedora 42 via RPM
2. Configure 16 MCP servers in claude_desktop_config.json
3. Open Cowork session
4. Observe: Chrome bridge fails, some MCPs missing, config may get wiped

Expected behavior

All MCP servers should work in Cowork same as Chat. Config should never be silently overwritten.