fix(core): preserve non-app MCP tools in apps mode

[karel-openai]

Summary

This fixes a regression where enabling Feature::Apps could hide non-codex_apps MCP tools (e.g. Notion MCP write tools) from the model tool list.

In built_tools, the apps path rebuilt mcp_tools from:

• selected MCP tools (if any), plus
• filtered codex_apps tools.

When there was no MCP tool selection yet, this effectively dropped non-codex_apps servers from model-visible tools.

Root Cause

built_tools applied apps filtering by constructing a reduced MCP map and assigning it back to mcp_tools.
That reduced map only guaranteed codex_apps tool inclusion, so tools from other MCP servers could disappear even though those servers were started and healthy.

Fix

• Introduce merge_apps_mode_mcp_tools(...) to merge app-filtered tools with selected tools.
• Preserve non-codex_apps MCP tools when there is no explicit MCP tool selection.
• Preserve explicit selection behavior when selection is present.

Tests

Added unit tests in codex-rs/core/src/codex.rs:

• apps_mode_keeps_non_codex_apps_mcp_tools_without_selection
• apps_mode_respects_explicit_tool_selection

Ran:

• cargo test -p codex-core apps_mode_keeps_non_codex_apps_mcp_tools_without_selection -- --nocapture
• cargo test -p codex-core apps_mode_respects_explicit_tool_selection -- --nocapture

User Impact

With apps enabled, MCP tools from non-app servers (including Notion MCP write tools) remain callable unless explicitly filtered by selection semantics.

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[mzeng-openai]

I think we should include non-apps MCP tools regardless of the current selection.