agentmemory connect zed overwrites existing Zed settings.json instead of merging context_servers

[IgorArkhipov]

Summary

Running agentmemory connect zed appears to overwrite the entire existing Zed config at ~/.config/zed/settings.json instead of preserving existing settings and only adding/updating the context_servers.agentmemory entry.

What happened

I ran:

agentmemory connect zed

The command reported success and created a backup:

→ Using MCP via ~/.config/zed/settings.json (key: context_servers).
Backup: /Users/<username>/.agentmemory/backups/zed-2026-06-20T03-15-54-964Z.json
zed → /Users/<username>/.config/zed/settings.json

But the existing /Users/<username>/.config/zed/settings.json contents were wiped and replaced with the new AgentMemory context server config:

{
  "context_servers": {
    "agentmemory": {
      "command": "npx",
      "args": ["-y", "@agentmemory/mcp"],
      "env": {
        "AGENTMEMORY_URL": "${AGENTMEMORY_URL:-http://localhost:3111}",
        "AGENTMEMORY_SECRET": "${AGENTMEMORY_SECRET:-}",
        "AGENTMEMORY_TOOLS": "${AGENTMEMORY_TOOLS:-all}"
      }
    }
  }
}

Expected behavior

agentmemory connect zed should preserve all existing Zed settings and merge/upsert only:

"context_servers": {
  "agentmemory": { ... }
}

Existing top-level settings and existing context_servers entries should remain intact.

Actual behavior

The command replaces the whole settings file, causing unrelated Zed preferences and existing context server settings to be lost.
A backup is created, but the command still reports success after destructive behavior.

Suggested fix

Parse the existing Zed settings file, merge context_servers.agentmemory into it, and write the merged result back.
If the existing settings file cannot be parsed, the command should fail safely or ask before replacing it.

A regression test would be useful for:

• preserving unrelated top-level Zed settings
• preserving existing context_servers entries
• updating an existing context_servers.agentmemory entry
• not overwriting the file when parsing fails