[app-server] Make sure that config writes preserve comments & order or configs (#7789)

Make sure that config writes preserve comments and order of configs by
utilizing the ConfigEditsBuilder in core.

Tested by running a real example and made sure that nothing in the
config file changes other than the configs to edit.

codex-rs/core/src/config/edit.rs

@@ -555,6 +555,14 @@ impl ConfigEditsBuilder {
         self
     }
 
+    pub fn with_edits<I>(mut self, edits: I) -> Self
+    where
+        I: IntoIterator<Item = ConfigEdit>,
+    {
+        self.edits.extend(edits);
+        self
+    }
+
     /// Apply edits on a blocking thread.
     pub fn apply_blocking(self) -> anyhow::Result<()> {
         apply_blocking(&self.codex_home, self.profile.as_deref(), &self.edits)
@@ -603,6 +611,24 @@ model_reasoning_effort = "high"
         assert_eq!(contents, expected);
     }
 
+    #[test]
+    fn builder_with_edits_applies_custom_paths() {
+        let tmp = tempdir().expect("tmpdir");
+        let codex_home = tmp.path();
+
+        ConfigEditsBuilder::new(codex_home)
+            .with_edits(vec![ConfigEdit::SetPath {
+                segments: vec!["enabled".to_string()],
+                value: value(true),
+            }])
+            .apply_blocking()
+            .expect("persist");
+
+        let contents =
+            std::fs::read_to_string(codex_home.join(CONFIG_TOML_FILE)).expect("read config");
+        assert_eq!(contents, "enabled = true\n");
+    }
+
     #[test]
     fn blocking_set_model_preserves_inline_table_contents() {
         let tmp = tempdir().expect("tmpdir");