[codex] reduce module visibility (#16978)

## Summary
- reduce public module visibility across Rust crates, preferring private
or crate-private modules with explicit crate-root public exports
- update external call sites and tests to use the intended public crate
APIs instead of reaching through module trees
- add the module visibility guideline to AGENTS.md

## Validation
- `cargo check --workspace --all-targets --message-format=short` passed
before the final fix/format pass
- `just fix` completed successfully
- `just fmt` completed successfully
- `git diff --check` passed

codex-rs/core/src/plugins/injection.rs

@@ -7,8 +7,8 @@ use codex_protocol::models::ResponseItem;
 use crate::connectors;
 use crate::plugins::PluginCapabilitySummary;
 use crate::plugins::render_explicit_plugin_instructions;
-use codex_mcp::mcp::CODEX_APPS_MCP_SERVER_NAME;
-use codex_mcp::mcp_connection_manager::ToolInfo;
+use codex_mcp::CODEX_APPS_MCP_SERVER_NAME;
+use codex_mcp::ToolInfo;
 
 pub(crate) fn build_plugin_injections(
     mentioned_plugins: &[PluginCapabilitySummary],