Installer adds hooks to both hooks.json and config.toml

[jiangjianzeng]

Summary

After installing codebase-memory-mcp, Codex starts with this warning:

loading hooks from both ~/.codex/hooks.json and ~/.codex/config.toml; prefer a single representation for this layer

It looks like the installer writes hook configuration into both hook representations at the same time.

What happened

The installation added a SessionStart hook to ~/.codex/config.toml:

[[hooks.SessionStart]]
matcher = "startup|resume|clear|compact"

[[hooks.SessionStart.hooks]]
type = "command"
command = 'echo "Code discovery: prefer codebase-memory-mcp (search_graph, trace_path, get_code_snippet, query_graph, search_code) over grep/file-read; run index_repository first if the project is not indexed."'
# <<< codebase-memory-mcp SessionStart <<<

At the same time, ~/.codex/hooks.json also contains hook definitions, including a matching SessionStart hook with the same message:

{
  "hooks": {
    "SessionStart": [
      {
        "matcher": "startup|resume|clear|compact",
        "hooks": [
          {
            "type": "command",
            "command": "echo \"Code discovery: prefer codebase-memory-mcp (search_graph, trace_path, get_code_snippet, query_graph, search_code) over grep/file-read; run index_repository first if the project is not indexed.\""
          }
        ]
      }
    ]
  }
}

This causes Codex to warn that hooks are being loaded from both hooks.json and config.toml.

Impact

For this specific hook, the impact is minor but visible:

• the startup/session hook message can appear more than once;
• Codex emits the warning about mixed hook representations;
• users may think their Codex or MCP setup is broken;
• if future hooks have side effects, duplicate hook sources could cause duplicate execution, slower startup, duplicated state writes, etc.

Expected behavior

The installer should prefer a single hook representation for the same layer, for example:

• write codebase-memory-mcp hooks only to ~/.codex/hooks.json if that file is already being used; or
• write only to ~/.codex/config.toml; or
• detect the existing representation and avoid adding the same hook to both places.

Suggested fix

During installation/setup, detect whether ~/.codex/hooks.json exists or whether Codex is already using TOML hooks, then install the SessionStart hook into only one location.

It may also be useful to add cleanup/migration logic that removes the duplicate codebase-memory-mcp SessionStart block from config.toml when the same hook already exists in hooks.json.

[sahil-mangla]

@DeusData can i work on this?