[MCP] Allow specifying cwd and additional env vars (#5246)

This makes stdio mcp servers more flexible by allowing users to specify
the cwd to run the server command from and adding additional environment
variables to be passed through to the server.

Example config using the test server in this repo:
```toml
[mcp_servers.test_stdio]
cwd = "/Users/<user>/code/codex/codex-rs"
command = "cargo"
args = ["run", "--bin", "test_stdio_server"]
env_vars = ["MCP_TEST_VALUE"]
```

@bolinfest I know you hate these env var tests but let's roll with this
for now. I may take a stab at the env guard + serial macro at some
point.

codex-rs/core/src/mcp_connection_manager.rs

@@ -10,6 +10,7 @@ use std::collections::HashMap;
 use std::collections::HashSet;
 use std::env;
 use std::ffi::OsString;
+use std::path::PathBuf;
 use std::sync::Arc;
 use std::time::Duration;
 
@@ -102,20 +103,25 @@ enum McpClientAdapter {
 }
 
 impl McpClientAdapter {
+    #[allow(clippy::too_many_arguments)]
     async fn new_stdio_client(
         use_rmcp_client: bool,
         program: OsString,
         args: Vec<OsString>,
         env: Option<HashMap<String, String>>,
+        env_vars: Vec<String>,
+        cwd: Option<PathBuf>,
         params: mcp_types::InitializeRequestParams,
         startup_timeout: Duration,
     ) -> Result<Self> {
         if use_rmcp_client {
-            let client = Arc::new(RmcpClient::new_stdio_client(program, args, env).await?);
+            let client =
+                Arc::new(RmcpClient::new_stdio_client(program, args, env, &env_vars, cwd).await?);
             client.initialize(params, Some(startup_timeout)).await?;
             Ok(McpClientAdapter::Rmcp(client))
         } else {
-            let client = Arc::new(McpClient::new_stdio_client(program, args, env).await?);
+            let client =
+                Arc::new(McpClient::new_stdio_client(program, args, env, &env_vars, cwd).await?);
             client.initialize(params, Some(startup_timeout)).await?;
             Ok(McpClientAdapter::Legacy(client))
         }
@@ -256,7 +262,13 @@ impl McpConnectionManager {
                 };
 
                 let client = match transport {
-                    McpServerTransportConfig::Stdio { command, args, env } => {
+                    McpServerTransportConfig::Stdio {
+                        command,
+                        args,
+                        env,
+                        env_vars,
+                        cwd,
+                    } => {
                         let command_os: OsString = command.into();
                         let args_os: Vec<OsString> = args.into_iter().map(Into::into).collect();
                         McpClientAdapter::new_stdio_client(
@@ -264,6 +276,8 @@ impl McpConnectionManager {
                             command_os,
                             args_os,
                             env,
+                            env_vars,
+                            cwd,
                             params,
                             startup_timeout,
                         )