diff --git a/code-rs/config/src/types.rs b/code-rs/config/src/types.rs
index 39fd0a442f5..d79b2a653ed 100644
--- a/code-rs/config/src/types.rs
+++ b/code-rs/config/src/types.rs
@@ -25,6 +25,7 @@ use std::collections::HashMap;
 use std::fmt;
 
 use schemars::JsonSchema;
+use serde::Deserializer;
 use serde::Deserialize;
 use serde::Serialize;
 
@@ -664,7 +665,7 @@ pub struct Tui {
     ///
     /// Using alternate screen provides a cleaner fullscreen experience but prevents
     /// scrollback in terminal multiplexers like Zellij that follow the xterm spec.
-    #[serde(default)]
+    #[serde(default, deserialize_with = "deserialize_alt_screen_mode")]
     pub alternate_screen: AltScreenMode,
 
     /// Ordered list of status line item identifiers.
@@ -692,7 +693,7 @@ pub struct Tui {
     ///
     /// When set, overrides automatic light/dark theme detection.
     /// Use `/theme` in the TUI or see `$CODEX_HOME/themes` for custom themes.
-    #[serde(default)]
+    #[serde(default, deserialize_with = "deserialize_tui_theme")]
     pub theme: Option<String>,
 
     /// Preferred layout for resume/fork session picker results.
@@ -740,6 +741,41 @@ pub struct ExternalConfigMigrationPrompts {
     pub project_last_prompted_at: BTreeMap<String, i64>,
 }
 
+fn deserialize_alt_screen_mode<'de, D>(deserializer: D) -> Result<AltScreenMode, D::Error>
+where
+    D: Deserializer<'de>,
+{
+    #[derive(Deserialize)]
+    #[serde(untagged)]
+    enum AltScreenCompat {
+        Mode(AltScreenMode),
+        LegacyBool(bool),
+    }
+
+    match AltScreenCompat::deserialize(deserializer)? {
+        AltScreenCompat::Mode(mode) => Ok(mode),
+        AltScreenCompat::LegacyBool(true) => Ok(AltScreenMode::Always),
+        AltScreenCompat::LegacyBool(false) => Ok(AltScreenMode::Never),
+    }
+}
+
+fn deserialize_tui_theme<'de, D>(deserializer: D) -> Result<Option<String>, D::Error>
+where
+    D: Deserializer<'de>,
+{
+    #[derive(Deserialize)]
+    #[serde(untagged)]
+    enum TuiThemeCompat {
+        Name(String),
+        LegacyTable { name: String },
+    }
+
+    Ok(Option::<TuiThemeCompat>::deserialize(deserializer)?.map(|theme| match theme {
+        TuiThemeCompat::Name(name) => name,
+        TuiThemeCompat::LegacyTable { name } => name,
+    }))
+}
+
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Default, JsonSchema)]
 #[schemars(deny_unknown_fields)]
 pub struct Notice {
diff --git a/code-rs/core/src/config/config_tests.rs b/code-rs/core/src/config/config_tests.rs
index 25f6697c7f5..cb2ecca6bd2 100644
--- a/code-rs/core/src/config/config_tests.rs
+++ b/code-rs/core/src/config/config_tests.rs
@@ -624,6 +624,53 @@ terminal_resize_reflow_max_rows = 9000
     );
 }
 
+#[test]
+fn config_toml_deserializes_legacy_tui_alternate_screen_bool() {
+    let enabled_toml = r#"
+[tui]
+alternate_screen = true
+"#;
+    let enabled_cfg: ConfigToml = toml::from_str(enabled_toml)
+        .expect("TOML deserialization should accept legacy alternate_screen bool");
+    assert_eq!(
+        enabled_cfg
+            .tui
+            .expect("tui config should deserialize")
+            .alternate_screen,
+        AltScreenMode::Always
+    );
+
+    let disabled_toml = r#"
+[tui]
+alternate_screen = false
+"#;
+    let disabled_cfg: ConfigToml = toml::from_str(disabled_toml)
+        .expect("TOML deserialization should accept legacy alternate_screen bool");
+    assert_eq!(
+        disabled_cfg
+            .tui
+            .expect("tui config should deserialize")
+            .alternate_screen,
+        AltScreenMode::Never
+    );
+}
+
+#[test]
+fn config_toml_deserializes_tui_alternate_screen_string_mode() {
+    let toml = r#"
+[tui]
+alternate_screen = "always"
+"#;
+    let cfg: ConfigToml = toml::from_str(toml)
+        .expect("TOML deserialization should accept alternate_screen string mode");
+    assert_eq!(
+        cfg.tui
+            .expect("tui config should deserialize")
+            .alternate_screen,
+        AltScreenMode::Always
+    );
+}
+
 #[tokio::test]
 async fn runtime_config_defaults_model_availability_nux() {
     let cfg = Config::load_from_base_config_with_overrides(
@@ -2155,6 +2202,21 @@ theme = "dracula"
     );
 }
 
+#[test]
+fn tui_theme_deserializes_legacy_table_from_toml() {
+    let cfg = r#"
+[tui.theme]
+name = "dark-oled-black-pro"
+is_dark = true
+"#;
+    let parsed = toml::from_str::<ConfigToml>(cfg)
+        .expect("TOML deserialization should accept legacy TUI theme table");
+    assert_eq!(
+        parsed.tui.as_ref().and_then(|t| t.theme.as_deref()),
+        Some("dark-oled-black-pro"),
+    );
+}
+
 #[test]
 fn tui_theme_defaults_to_none() {
     let cfg = r#"
diff --git a/code-rs/features/src/lib.rs b/code-rs/features/src/lib.rs
index 6c8ce49894d..d40ac5447ae 100644
--- a/code-rs/features/src/lib.rs
+++ b/code-rs/features/src/lib.rs
@@ -422,6 +422,9 @@ impl Features {
                 "image_detail_original" => {
                     continue;
                 }
+                "skills" => {
+                    continue;
+                }
                 "use_legacy_landlock" => {
                     self.record_legacy_usage_force(
                         "features.use_legacy_landlock",
diff --git a/code-rs/features/src/tests.rs b/code-rs/features/src/tests.rs
index 5464fa7a61a..c85a09ab208 100644
--- a/code-rs/features/src/tests.rs
+++ b/code-rs/features/src/tests.rs
@@ -66,6 +66,14 @@ fn image_detail_original_is_removed_and_disabled_by_default() {
     assert_eq!(Feature::ImageDetailOriginal.default_enabled(), false);
 }
 
+#[test]
+fn skills_feature_key_is_accepted_as_removed_noop() {
+    let mut features = Features::with_defaults();
+    features.apply_map(&BTreeMap::from([("skills".to_string(), true)]));
+
+    assert_eq!(features.enabled(Feature::ShellTool), true);
+}
+
 #[test]
 fn code_mode_only_requires_code_mode() {
     let mut features = Features::with_defaults();