feat: make cwd a required field of Config so we stop assuming std::env::current_dir() in a session (#800)

In order to expose Codex via an MCP server, I realized that we should be
taking `cwd` as a parameter rather than assuming
`std::env::current_dir()` as the `cwd`. Specifically, the user may want
to start a session in a directory other than the one where the MCP
server has been started.

This PR makes `cwd: PathBuf` a required field of `Session` and threads
it all the way through, though I think there is still an issue with not
honoring `workdir` for `apply_patch`, which is something we also had to
fix in the TypeScript version: https://github.com/openai/codex/pull/556.

This also adds `-C`/`--cd` to change the cwd via the command line.

To test, I ran:

```
cargo run --bin codex -- exec -C /tmp 'show the output of ls'
```

and verified it showed the contents of my `/tmp` folder instead of
`$PWD`.

codex-rs/core/src/models.rs

@@ -102,6 +102,20 @@ impl From<Vec<InputItem>> for ResponseInputItem {
     }
 }
 
+/// If the `name` of a `ResponseItem::FunctionCall` is either `container.exec`
+/// or shell`, the `arguments` field should deserialize to this struct.
+#[derive(Deserialize, Debug, Clone, PartialEq)]
+pub struct ShellToolCallParams {
+    pub command: Vec<String>,
+    pub workdir: Option<String>,
+
+    /// This is the maximum time in seconds that the command is allowed to run.
+    #[serde(rename = "timeout")]
+    // The wire format uses `timeout`, which has ambiguous units, so we use
+    // `timeout_ms` as the field name so it is clear in code.
+    pub timeout_ms: Option<u64>,
+}
+
 #[expect(dead_code)]
 #[derive(Deserialize, Debug, Clone)]
 pub struct FunctionCallOutputPayload {
@@ -183,4 +197,23 @@ mod tests {
 
         assert_eq!(v.get("output").unwrap().as_str().unwrap(), "bad");
     }
+
+    #[test]
+    fn deserialize_shell_tool_call_params() {
+        let json = r#"{
+            "command": ["ls", "-l"],
+            "workdir": "/tmp",
+            "timeout": 1000
+        }"#;
+
+        let params: ShellToolCallParams = serde_json::from_str(json).unwrap();
+        assert_eq!(
+            ShellToolCallParams {
+                command: vec!["ls".to_string(), "-l".to_string()],
+                workdir: Some("/tmp".to_string()),
+                timeout_ms: Some(1000),
+            },
+            params
+        );
+    }
 }