diff --git a/codex-rs/app-server/tests/suite/v2/turn_start.rs b/codex-rs/app-server/tests/suite/v2/turn_start.rs
index 62192ebd08f0..314be8a6ff68 100644
--- a/codex-rs/app-server/tests/suite/v2/turn_start.rs
+++ b/codex-rs/app-server/tests/suite/v2/turn_start.rs
@@ -2476,13 +2476,26 @@ async fn turn_start_streams_apply_patch_change_updates_v2() -> Result<()> {
         &server.uri(),
         "never",
         &BTreeMap::from([
-            (Feature::ApplyPatchFreeform, true),
             (Feature::ApplyPatchStreamingEvents, true),
             (Feature::Plugins, false),
             (Feature::RemoteModels, false),
             (Feature::ShellSnapshot, false),
         ]),
     )?;
+    write_models_cache(&codex_home)?;
+    let cache_path = codex_home.join("models_cache.json");
+    let mut cache: serde_json::Value =
+        serde_json::from_str(&std::fs::read_to_string(&cache_path)?)?;
+    let models = cache["models"]
+        .as_array_mut()
+        .expect("models_cache.json models should be an array");
+    let model = models
+        .first_mut()
+        .expect("models_cache.json should contain at least one model");
+    model["slug"] = serde_json::Value::from("mock-model");
+    model["display_name"] = serde_json::Value::from("mock-model");
+    model["apply_patch_tool_type"] = serde_json::Value::from("freeform");
+    std::fs::write(&cache_path, serde_json::to_string_pretty(&cache)?)?;
 
     let mut mcp = McpProcess::new(&codex_home).await?;
     timeout(DEFAULT_READ_TIMEOUT, mcp.initialize()).await??;
diff --git a/codex-rs/core/config.schema.json b/codex-rs/core/config.schema.json
index 84ce98ffc5cd..2c0acbf8958d 100644
--- a/codex-rs/core/config.schema.json
+++ b/codex-rs/core/config.schema.json
@@ -457,9 +457,6 @@
             "in_app_browser": {
               "type": "boolean"
             },
-            "include_apply_patch_tool": {
-              "type": "boolean"
-            },
             "js_repl": {
               "type": "boolean"
             },
@@ -4224,9 +4221,6 @@
         "in_app_browser": {
           "type": "boolean"
         },
-        "include_apply_patch_tool": {
-          "type": "boolean"
-        },
         "js_repl": {
           "type": "boolean"
         },
diff --git a/codex-rs/core/src/config/config_tests.rs b/codex-rs/core/src/config/config_tests.rs
index c2ef25e6cbd0..571f88273578 100644
--- a/codex-rs/core/src/config/config_tests.rs
+++ b/codex-rs/core/src/config/config_tests.rs
@@ -4320,7 +4320,6 @@ async fn feature_table_overrides_legacy_flags() -> std::io::Result<()> {
     .await?;
 
     assert!(!config.features.enabled(Feature::ApplyPatchFreeform));
-    assert!(!config.include_apply_patch_tool);
 
     Ok(())
 }
@@ -7505,7 +7504,6 @@ async fn test_precedence_fixture_with_o3_profile() -> std::io::Result<()> {
             compact_prompt: None,
             forced_chatgpt_workspace_id: None,
             forced_login_method: None,
-            include_apply_patch_tool: true,
             web_search_mode: Constrained::allow_any(WebSearchMode::Cached),
             web_search_config: None,
             use_experimental_unified_exec_tool: !cfg!(windows),
@@ -7954,7 +7952,6 @@ async fn test_precedence_fixture_with_gpt3_profile() -> std::io::Result<()> {
         compact_prompt: None,
         forced_chatgpt_workspace_id: None,
         forced_login_method: None,
-        include_apply_patch_tool: true,
         web_search_mode: Constrained::allow_any(WebSearchMode::Cached),
         web_search_config: None,
         use_experimental_unified_exec_tool: !cfg!(windows),
@@ -8117,7 +8114,6 @@ async fn test_precedence_fixture_with_zdr_profile() -> std::io::Result<()> {
         compact_prompt: None,
         forced_chatgpt_workspace_id: None,
         forced_login_method: None,
-        include_apply_patch_tool: true,
         web_search_mode: Constrained::allow_any(WebSearchMode::Cached),
         web_search_config: None,
         use_experimental_unified_exec_tool: !cfg!(windows),
@@ -8265,7 +8261,6 @@ async fn test_precedence_fixture_with_gpt5_profile() -> std::io::Result<()> {
         compact_prompt: None,
         forced_chatgpt_workspace_id: None,
         forced_login_method: None,
-        include_apply_patch_tool: true,
         web_search_mode: Constrained::allow_any(WebSearchMode::Cached),
         web_search_config: None,
         use_experimental_unified_exec_tool: !cfg!(windows),
diff --git a/codex-rs/core/src/config/managed_features.rs b/codex-rs/core/src/config/managed_features.rs
index 78b88d2f3ab9..480225fb99ac 100644
--- a/codex-rs/core/src/config/managed_features.rs
+++ b/codex-rs/core/src/config/managed_features.rs
@@ -348,12 +348,10 @@ pub(crate) fn validate_feature_requirements_in_config_toml(
         let configured_features = Features::from_sources(
             FeatureConfigSource {
                 features: cfg.features.as_ref(),
-                include_apply_patch_tool: None,
                 experimental_use_unified_exec_tool: cfg.experimental_use_unified_exec_tool,
             },
             FeatureConfigSource {
                 features: profile.features.as_ref(),
-                include_apply_patch_tool: None,
                 experimental_use_unified_exec_tool: profile.experimental_use_unified_exec_tool,
             },
             FeatureOverrides::default(),
diff --git a/codex-rs/core/src/config/mod.rs b/codex-rs/core/src/config/mod.rs
index 16d8a57b3052..fa48bfde867f 100644
--- a/codex-rs/core/src/config/mod.rs
+++ b/codex-rs/core/src/config/mod.rs
@@ -764,11 +764,6 @@ pub struct Config {
     /// When set, restricts the login mechanism users may use.
     pub forced_login_method: Option<ForcedLoginMethod>,
 
-    /// Include the `apply_patch` tool for models that benefit from invoking
-    /// file edits as a structured tool call. When unset, this falls back to the
-    /// model info's default preference.
-    pub include_apply_patch_tool: bool,
-
     /// Explicit or feature-derived web search mode.
     pub web_search_mode: Constrained<WebSearchMode>,
 
@@ -2301,12 +2296,10 @@ impl Config {
         let configured_features = Features::from_sources(
             FeatureConfigSource {
                 features: cfg.features.as_ref(),
-                include_apply_patch_tool: None,
                 experimental_use_unified_exec_tool: cfg.experimental_use_unified_exec_tool,
             },
             FeatureConfigSource {
                 features: config_profile.features.as_ref(),
-                include_apply_patch_tool: None,
                 experimental_use_unified_exec_tool: config_profile
                     .experimental_use_unified_exec_tool,
             },
@@ -2845,7 +2838,6 @@ impl Config {
             config
         };
 
-        let include_apply_patch_tool_flag = features.enabled(Feature::ApplyPatchFreeform);
         let use_experimental_unified_exec_tool = features.enabled(Feature::UnifiedExec);
 
         let forced_chatgpt_workspace_id = cfg
@@ -3257,7 +3249,6 @@ impl Config {
             experimental_thread_store: thread_store_config(cfg.experimental_thread_store),
             forced_chatgpt_workspace_id,
             forced_login_method,
-            include_apply_patch_tool: include_apply_patch_tool_flag,
             web_search_mode: constrained_web_search_mode.value,
             web_search_config,
             use_experimental_unified_exec_tool,
diff --git a/codex-rs/core/src/guardian/review_session.rs b/codex-rs/core/src/guardian/review_session.rs
index d3fae0f2e567..253ead5b41f3 100644
--- a/codex-rs/core/src/guardian/review_session.rs
+++ b/codex-rs/core/src/guardian/review_session.rs
@@ -151,7 +151,6 @@ struct GuardianReviewSessionReuseKey {
     main_execve_wrapper_exe: Option<PathBuf>,
     zsh_path: Option<PathBuf>,
     features: ManagedFeatures,
-    include_apply_patch_tool: bool,
     use_experimental_unified_exec_tool: bool,
 }
 
@@ -176,7 +175,6 @@ impl GuardianReviewSessionReuseKey {
             main_execve_wrapper_exe: spawn_config.main_execve_wrapper_exe.clone(),
             zsh_path: spawn_config.zsh_path.clone(),
             features: spawn_config.features.clone(),
-            include_apply_patch_tool: spawn_config.include_apply_patch_tool,
             use_experimental_unified_exec_tool: spawn_config.use_experimental_unified_exec_tool,
         }
     }
diff --git a/codex-rs/core/src/tools/spec_tests.rs b/codex-rs/core/src/tools/spec_tests.rs
index ca8739ccff4c..8653810ba470 100644
--- a/codex-rs/core/src/tools/spec_tests.rs
+++ b/codex-rs/core/src/tools/spec_tests.rs
@@ -1162,7 +1162,6 @@ async fn test_mcp_tool_array_without_items_gets_default_string_items() {
     let model_info = construct_model_info_offline("gpt-5.4", &config);
     let mut features = Features::with_defaults();
     features.enable(Feature::UnifiedExec);
-    features.enable(Feature::ApplyPatchFreeform);
     let available_models = Vec::new();
     let tools_config = ToolsConfig::new(&ToolsConfigParams {
         model_info: &model_info,
diff --git a/codex-rs/core/tests/common/test_codex.rs b/codex-rs/core/tests/common/test_codex.rs
index fd53e828a9c9..947111d3fc9a 100644
--- a/codex-rs/core/tests/common/test_codex.rs
+++ b/codex-rs/core/tests/common/test_codex.rs
@@ -24,7 +24,6 @@ use codex_exec_server::CreateDirectoryOptions;
 use codex_exec_server::ExecutorFileSystem;
 use codex_exec_server::RemoveOptions;
 use codex_extension_api::empty_extension_registry;
-use codex_features::Feature;
 use codex_login::CodexAuth;
 use codex_model_provider_info::ModelProviderInfo;
 use codex_model_provider_info::built_in_model_providers;
@@ -581,12 +580,6 @@ impl TestCodexBuilder {
         }
         ensure_test_model_catalog(&mut config)?;
 
-        if config.include_apply_patch_tool {
-            config.features.enable(Feature::ApplyPatchFreeform)?;
-        } else {
-            config.features.disable(Feature::ApplyPatchFreeform)?;
-        }
-
         Ok((config, cwd))
     }
 }
diff --git a/codex-rs/core/tests/suite/apply_patch_cli.rs b/codex-rs/core/tests/suite/apply_patch_cli.rs
index b692d3256857..9185b8a7bd47 100644
--- a/codex-rs/core/tests/suite/apply_patch_cli.rs
+++ b/codex-rs/core/tests/suite/apply_patch_cli.rs
@@ -59,9 +59,7 @@ pub async fn apply_patch_harness() -> Result<TestCodexHarness> {
 async fn apply_patch_harness_with(
     configure: impl FnOnce(TestCodexBuilder) -> TestCodexBuilder,
 ) -> Result<TestCodexHarness> {
-    let builder = configure(test_codex()).with_config(|config| {
-        config.include_apply_patch_tool = true;
-    });
+    let builder = configure(test_codex());
     // Box harness construction so apply_patch_cli tests do not inline the
     // full test-thread startup path into each test future.
     Box::pin(TestCodexHarness::with_remote_env_builder(builder)).await
@@ -989,15 +987,7 @@ async fn apply_patch_cli_verification_failure_has_no_side_effects(
 ) -> Result<()> {
     skip_if_no_network!(Ok(()));
 
-    let harness = apply_patch_harness_with(|builder| {
-        builder.with_config(|config| {
-            config
-                .features
-                .enable(Feature::ApplyPatchFreeform)
-                .expect("test config should allow feature update");
-        })
-    })
-    .await?;
+    let harness = apply_patch_harness().await?;
 
     // Compose a patch that would create a file, then fail verification on an update.
     let call_id = "apply-partial-no-side-effects";
diff --git a/codex-rs/core/tests/suite/approvals.rs b/codex-rs/core/tests/suite/approvals.rs
index 439eab5be2ce..5045755e3225 100644
--- a/codex-rs/core/tests/suite/approvals.rs
+++ b/codex-rs/core/tests/suite/approvals.rs
@@ -1408,7 +1408,7 @@ fn scenarios() -> Vec<ScenarioSpec> {
                 content: "freeform-patch-danger",
             },
             sandbox_permissions: SandboxPermissions::UseDefault,
-            features: vec![Feature::ApplyPatchFreeform],
+            features: vec![],
             model_override: Some("gpt-5.4"),
             outcome: Outcome::Auto,
             expectation: Expectation::PatchApplied {
diff --git a/codex-rs/core/tests/suite/code_mode.rs b/codex-rs/core/tests/suite/code_mode.rs
index af63d092f8cc..ff7640f05e3f 100644
--- a/codex-rs/core/tests/suite/code_mode.rs
+++ b/codex-rs/core/tests/suite/code_mode.rs
@@ -144,13 +144,11 @@ async fn run_code_mode_turn(
     server: &MockServer,
     prompt: &str,
     code: &str,
-    include_apply_patch: bool,
 ) -> Result<(TestCodex, ResponseMock)> {
     let mut builder = test_codex()
         .with_model("test-gpt-5.1-codex")
         .with_config(move |config| {
             let _ = config.features.enable(Feature::CodeMode);
-            config.include_apply_patch_tool = include_apply_patch;
         });
     let test = builder.build(server).await?;
 
@@ -291,7 +289,6 @@ async fn code_mode_can_return_exec_command_output() -> Result<()> {
         r#"
 text(JSON.stringify(await tools.exec_command({ cmd: "printf code_mode_exec_marker" })));
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -541,7 +538,6 @@ const result = await tools.update_plan({
 });
 text(JSON.stringify(result));
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -666,7 +662,6 @@ text(JSON.stringify(await tools.exec_command({
   max_output_tokens: 100
 })));
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -705,7 +700,6 @@ text("before crash");
 text("still before crash");
 throw new Error("boom");
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -752,7 +746,6 @@ try {
   text(`caught:${error?.message ?? String(error)}`);
 }
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -1769,7 +1762,6 @@ async fn code_mode_can_output_serialized_text_via_global_helper() -> Result<()>
         r#"
 text({ json: true });
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -1801,7 +1793,6 @@ async fn code_mode_can_resume_after_set_timeout() -> Result<()> {
 await new Promise((resolve) => setTimeout(resolve, 10));
 text("timer done");
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -1830,7 +1821,6 @@ notify("code_mode_notify_marker");
 await tools.test_sync_tool({});
 text("done");
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -1868,7 +1858,6 @@ text("before");
 exit();
 text("after");
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -1907,7 +1896,6 @@ const circular = {};
 circular.self = circular;
 text(circular);
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -1947,7 +1935,6 @@ async fn code_mode_can_output_images_via_global_helper() -> Result<()> {
 image("https://example.com/image.jpg");
 image("data:image/png;base64,AAA");
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
@@ -2137,13 +2124,8 @@ async fn code_mode_can_apply_patch_via_nested_tool() -> Result<()> {
     );
     let code = format!("text(await tools.apply_patch({patch:?}));\n");
 
-    let (test, second_mock) = run_code_mode_turn(
-        &server,
-        "use exec to run apply_patch",
-        &code,
-        /*include_apply_patch*/ true,
-    )
-    .await?;
+    let (test, second_mock) =
+        run_code_mode_turn(&server, "use exec to run apply_patch", &code).await?;
 
     let req = second_mock.single_request();
     let items = custom_tool_output_items(&req, "call-1");
@@ -2465,13 +2447,8 @@ const tool = ALL_TOOLS.find(({ name }) => name === "view_image");
 text(JSON.stringify(tool));
 "#;
 
-    let (_test, second_mock) = run_code_mode_turn(
-        &server,
-        "use exec to inspect ALL_TOOLS",
-        code,
-        /*include_apply_patch*/ false,
-    )
-    .await?;
+    let (_test, second_mock) =
+        run_code_mode_turn(&server, "use exec to inspect ALL_TOOLS", code).await?;
 
     let req = second_mock.single_request();
     let (output, success) = custom_tool_output_body_and_success(&req, "call-1");
@@ -2890,7 +2867,6 @@ text(JSON.stringify({
   waited_long_enough: end_ms - start_ms >= 100,
 }));
 "#,
-        /*include_apply_patch*/ false,
     )
     .await?;
 
diff --git a/codex-rs/core/tests/suite/codex_delegate.rs b/codex-rs/core/tests/suite/codex_delegate.rs
index cc31aa5c7782..f5db9856df2f 100644
--- a/codex-rs/core/tests/suite/codex_delegate.rs
+++ b/codex-rs/core/tests/suite/codex_delegate.rs
@@ -153,7 +153,6 @@ async fn codex_delegate_forwards_patch_approval_and_proceeds_on_decision() {
             .permissions
             .set_permission_profile(PermissionProfile::read_only())
             .expect("set permission profile");
-        config.include_apply_patch_tool = true;
     });
     let test = builder.build(&server).await.expect("build test codex");
 
diff --git a/codex-rs/core/tests/suite/hooks.rs b/codex-rs/core/tests/suite/hooks.rs
index f059998052da..53649afff849 100644
--- a/codex-rs/core/tests/suite/hooks.rs
+++ b/codex-rs/core/tests/suite/hooks.rs
@@ -1658,7 +1658,6 @@ async fn permission_request_hook_allows_apply_patch_with_write_alias() -> Result
             }
         })
         .with_config(|config| {
-            config.include_apply_patch_tool = true;
             trust_discovered_hooks(config);
         });
     let test = builder.build(&server).await?;
@@ -2880,7 +2879,6 @@ async fn pre_tool_use_blocks_apply_patch_before_execution() -> Result<()> {
             }
         })
         .with_config(|config| {
-            config.include_apply_patch_tool = true;
             trust_discovered_hooks(config);
         });
     let test = builder.build(&server).await?;
@@ -2959,7 +2957,6 @@ async fn pre_tool_use_rewrites_apply_patch_before_execution() -> Result<()> {
             }
         })
         .with_config(|config| {
-            config.include_apply_patch_tool = true;
             trust_discovered_hooks(config);
         });
     let test = builder.build(&server).await?;
@@ -3025,7 +3022,6 @@ async fn pre_tool_use_blocks_apply_patch_with_write_alias() -> Result<()> {
             }
         })
         .with_config(|config| {
-            config.include_apply_patch_tool = true;
             trust_discovered_hooks(config);
         });
     let test = builder.build(&server).await?;
@@ -3627,7 +3623,6 @@ async fn post_tool_use_records_additional_context_for_apply_patch() -> Result<()
             }
         })
         .with_config(|config| {
-            config.include_apply_patch_tool = true;
             trust_discovered_hooks(config);
         });
     let test = builder.build(&server).await?;
@@ -3715,7 +3710,6 @@ async fn post_tool_use_records_apply_patch_context_with_edit_alias() -> Result<(
             }
         })
         .with_config(|config| {
-            config.include_apply_patch_tool = true;
             trust_discovered_hooks(config);
         });
     let test = builder.build(&server).await?;
diff --git a/codex-rs/core/tests/suite/prompt_caching.rs b/codex-rs/core/tests/suite/prompt_caching.rs
index 5b861ab2193e..f887131eef95 100644
--- a/codex-rs/core/tests/suite/prompt_caching.rs
+++ b/codex-rs/core/tests/suite/prompt_caching.rs
@@ -231,10 +231,6 @@ async fn gpt_5_tools_without_apply_patch_append_apply_patch_instructions() -> an
     let TestCodex { codex, .. } = test_codex()
         .with_config(|config| {
             config.user_instructions = Some("be consistent and helpful".to_string());
-            config
-                .features
-                .disable(Feature::ApplyPatchFreeform)
-                .expect("test config should allow feature update");
             config
                 .features
                 .enable(Feature::CollaborationModes)
diff --git a/codex-rs/core/tests/suite/remote_env.rs b/codex-rs/core/tests/suite/remote_env.rs
index 9c3414baeb27..e19379ffc8c2 100644
--- a/codex-rs/core/tests/suite/remote_env.rs
+++ b/codex-rs/core/tests/suite/remote_env.rs
@@ -347,9 +347,7 @@ async fn apply_patch_freeform_routes_to_selected_remote_environment() -> Result<
     };
 
     let server = start_mock_server().await;
-    let mut builder = test_codex().with_config(|config| {
-        config.include_apply_patch_tool = true;
-    });
+    let mut builder = test_codex();
     let test = builder.build_with_remote_and_local_env(&server).await?;
     let local_cwd = TempDir::new()?;
     let file_name = "apply_patch_remote_freeform.txt";
@@ -435,7 +433,6 @@ async fn apply_patch_approvals_are_remembered_per_environment() -> Result<()> {
 
     let server = start_mock_server().await;
     let mut builder = test_codex().with_config(|config| {
-        config.include_apply_patch_tool = true;
         config.permissions.approval_policy = Constrained::allow_any(AskForApproval::OnRequest);
         config.approvals_reviewer = ApprovalsReviewer::User;
     });
diff --git a/codex-rs/core/tests/suite/request_permissions_tool.rs b/codex-rs/core/tests/suite/request_permissions_tool.rs
index 30b887ab0889..cb1324396677 100644
--- a/codex-rs/core/tests/suite/request_permissions_tool.rs
+++ b/codex-rs/core/tests/suite/request_permissions_tool.rs
@@ -340,7 +340,6 @@ async fn apply_patch_after_request_permissions(strict_auto_review: bool) -> Resu
     let permission_profile_for_config = permission_profile.clone();
 
     let mut builder = test_codex().with_config(move |config| {
-        config.include_apply_patch_tool = true;
         config.permissions.approval_policy = Constrained::allow_any(approval_policy);
         config
             .permissions
diff --git a/codex-rs/core/tests/suite/shell_command.rs b/codex-rs/core/tests/suite/shell_command.rs
index 1b3b3d0b403e..eb545fce0b9a 100644
--- a/codex-rs/core/tests/suite/shell_command.rs
+++ b/codex-rs/core/tests/suite/shell_command.rs
@@ -61,9 +61,7 @@ fn shell_responses(call_id: &str, command: &str, login: Option<bool>) -> Vec<Str
 async fn shell_command_harness_with(
     configure: impl FnOnce(TestCodexBuilder) -> TestCodexBuilder,
 ) -> Result<TestCodexHarness> {
-    let builder = configure(test_codex()).with_config(|config| {
-        config.include_apply_patch_tool = true;
-    });
+    let builder = configure(test_codex());
     TestCodexHarness::with_builder(builder).await
 }
 
diff --git a/codex-rs/core/tests/suite/shell_serialization.rs b/codex-rs/core/tests/suite/shell_serialization.rs
index 56afa59b739f..dbe4957ecb12 100644
--- a/codex-rs/core/tests/suite/shell_serialization.rs
+++ b/codex-rs/core/tests/suite/shell_serialization.rs
@@ -72,15 +72,10 @@ fn shell_responses(
 fn configure_shell_model(
     builder: TestCodexBuilder,
     output_type: ShellModelOutput,
-    include_apply_patch_tool: bool,
 ) -> TestCodexBuilder {
-    let builder = match output_type {
+    match output_type {
         ShellModelOutput::ShellCommand => builder.with_model("test-gpt-5-codex"),
-    };
-
-    builder.with_config(move |config| {
-        config.include_apply_patch_tool = include_apply_patch_tool;
-    })
+    }
 }
 
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
@@ -91,11 +86,7 @@ async fn shell_output_is_structured_with_freeform_apply_patch(
     skip_if_no_network!(Ok(()));
 
     let server = start_mock_server().await;
-    let mut builder = configure_shell_model(
-        test_codex(),
-        output_type,
-        /*include_apply_patch_tool*/ true,
-    );
+    let mut builder = configure_shell_model(test_codex(), output_type);
     let test = builder.build(&server).await?;
 
     let call_id = "shell-structured";
@@ -139,11 +130,7 @@ async fn shell_output_structures_fixture_with_serialization(
     skip_if_no_network!(Ok(()));
 
     let server = start_mock_server().await;
-    let mut builder = configure_shell_model(
-        test_codex(),
-        output_type,
-        /*include_apply_patch_tool*/ true,
-    );
+    let mut builder = configure_shell_model(test_codex(), output_type);
     let test = builder.build(&server).await?;
 
     let fixture_path = test.cwd.path().join("fixture.json");
@@ -200,11 +187,7 @@ async fn shell_output_for_freeform_tool_records_duration(
     skip_if_no_network!(Ok(()));
 
     let server = start_mock_server().await;
-    let mut builder = configure_shell_model(
-        test_codex(),
-        output_type,
-        /*include_apply_patch_tool*/ true,
-    );
+    let mut builder = configure_shell_model(test_codex(), output_type);
     let test = builder.build(&server).await?;
 
     let call_id = "shell-structured";
@@ -474,11 +457,7 @@ async fn shell_output_is_structured_for_nonzero_exit(output_type: ShellModelOutp
     skip_if_no_network!(Ok(()));
 
     let server = start_mock_server().await;
-    let mut builder = test_codex()
-        .with_model("gpt-5.4")
-        .with_config(move |config| {
-            config.include_apply_patch_tool = true;
-        });
+    let mut builder = test_codex().with_model("gpt-5.4");
     let test = builder.build(&server).await?;
 
     let call_id = "shell-nonzero-exit";
@@ -512,9 +491,7 @@ async fn shell_command_output_is_freeform() -> Result<()> {
     skip_if_no_network!(Ok(()));
 
     let server = start_mock_server().await;
-    let mut builder = test_codex().with_config(move |config| {
-        config.include_apply_patch_tool = true;
-    });
+    let mut builder = test_codex();
     let test = builder.build(&server).await?;
 
     let call_id = "shell-command";
diff --git a/codex-rs/core/tests/suite/shell_snapshot.rs b/codex-rs/core/tests/suite/shell_snapshot.rs
index f757fa322a59..49ef4956cde4 100644
--- a/codex-rs/core/tests/suite/shell_snapshot.rs
+++ b/codex-rs/core/tests/suite/shell_snapshot.rs
@@ -531,7 +531,6 @@ async fn shell_command_snapshot_still_intercepts_apply_patch() -> Result<()> {
             .features
             .enable(Feature::ShellSnapshot)
             .expect("test config should allow feature update");
-        config.include_apply_patch_tool = true;
     });
     let harness = TestCodexHarness::with_builder(builder).await?;
 
diff --git a/codex-rs/core/tests/suite/tool_harness.rs b/codex-rs/core/tests/suite/tool_harness.rs
index ac41d06c3f2b..38843f2d83a1 100644
--- a/codex-rs/core/tests/suite/tool_harness.rs
+++ b/codex-rs/core/tests/suite/tool_harness.rs
@@ -3,7 +3,6 @@
 use std::fs;
 
 use assert_matches::assert_matches;
-use codex_features::Feature;
 use codex_protocol::items::TurnItem;
 use codex_protocol::models::PermissionProfile;
 use codex_protocol::plan_tool::StepStatus;
@@ -324,12 +323,7 @@ async fn apply_patch_tool_executes_and_emits_patch_events() -> anyhow::Result<()
 
     let server = start_mock_server().await;
 
-    let mut builder = test_codex().with_config(|config| {
-        config
-            .features
-            .enable(Feature::ApplyPatchFreeform)
-            .expect("test config should allow feature update");
-    });
+    let mut builder = test_codex();
     let TestCodex {
         codex,
         cwd,
@@ -467,12 +461,7 @@ async fn apply_patch_reports_parse_diagnostics() -> anyhow::Result<()> {
 
     let server = start_mock_server().await;
 
-    let mut builder = test_codex().with_config(|config| {
-        config
-            .features
-            .enable(Feature::ApplyPatchFreeform)
-            .expect("test config should allow feature update");
-    });
+    let mut builder = test_codex();
     let TestCodex {
         codex,
         cwd,
diff --git a/codex-rs/core/tests/suite/tools.rs b/codex-rs/core/tests/suite/tools.rs
index 0f46e503867f..7b523a4686ff 100644
--- a/codex-rs/core/tests/suite/tools.rs
+++ b/codex-rs/core/tests/suite/tools.rs
@@ -71,7 +71,6 @@ async fn empty_turn_environments_omits_environment_backed_tools() -> Result<()>
             .features
             .enable(Feature::UnifiedExec)
             .expect("unified exec should enable for test");
-        config.include_apply_patch_tool = true;
     });
     let test = builder.build(&server).await?;
 
diff --git a/codex-rs/core/tests/suite/unified_exec.rs b/codex-rs/core/tests/suite/unified_exec.rs
index 231d14f77024..eeccd5b46532 100644
--- a/codex-rs/core/tests/suite/unified_exec.rs
+++ b/codex-rs/core/tests/suite/unified_exec.rs
@@ -235,7 +235,6 @@ async fn unified_exec_intercepts_apply_patch_exec_command() -> Result<()> {
     skip_if_windows!(Ok(()));
 
     let builder = test_codex().with_config(|config| {
-        config.include_apply_patch_tool = true;
         config.use_experimental_unified_exec_tool = true;
         if let Err(err) = config.features.enable(Feature::UnifiedExec) {
             panic!("test config should allow feature update: {err}");
diff --git a/codex-rs/features/src/legacy.rs b/codex-rs/features/src/legacy.rs
index c3dcb089a5cb..1a8b3d24dc18 100644
--- a/codex-rs/features/src/legacy.rs
+++ b/codex-rs/features/src/legacy.rs
@@ -21,10 +21,6 @@ const ALIASES: &[Alias] = &[
         legacy_key: "experimental_use_unified_exec_tool",
         feature: Feature::UnifiedExec,
     },
-    Alias {
-        legacy_key: "include_apply_patch_tool",
-        feature: Feature::ApplyPatchFreeform,
-    },
     Alias {
         legacy_key: "request_permissions",
         feature: Feature::ExecPermissionApprovals,
@@ -67,18 +63,11 @@ pub(crate) fn feature_for_key(key: &str) -> Option<Feature> {
 
 #[derive(Debug, Default)]
 pub(crate) struct LegacyFeatureToggles {
-    pub include_apply_patch_tool: Option<bool>,
     pub experimental_use_unified_exec_tool: Option<bool>,
 }
 
 impl LegacyFeatureToggles {
     pub fn apply(self, features: &mut Features) {
-        set_if_some(
-            features,
-            Feature::ApplyPatchFreeform,
-            self.include_apply_patch_tool,
-            "include_apply_patch_tool",
-        );
         set_if_some(
             features,
             Feature::UnifiedExec,
diff --git a/codex-rs/features/src/lib.rs b/codex-rs/features/src/lib.rs
index da74d21e94a0..194ad8b6c206 100644
--- a/codex-rs/features/src/lib.rs
+++ b/codex-rs/features/src/lib.rs
@@ -99,7 +99,7 @@ pub enum Feature {
     ShellZshFork,
     /// Reflow transcript scrollback when the terminal is resized.
     TerminalResizeReflow,
-    /// Include the freeform apply_patch tool.
+    /// Removed compatibility flag for the deleted apply_patch fallback feature.
     ApplyPatchFreeform,
     /// Stream structured progress while apply_patch input is being generated.
     ApplyPatchStreamingEvents,
@@ -292,7 +292,6 @@ pub struct FeatureOverrides {
 #[derive(Debug, Clone, Copy, Default)]
 pub struct FeatureConfigSource<'a> {
     pub features: Option<&'a FeaturesToml>,
-    pub include_apply_patch_tool: Option<bool>,
     pub experimental_use_unified_exec_tool: Option<bool>,
 }
 
@@ -424,6 +423,9 @@ impl Features {
                 "remote_control" => {
                     continue;
                 }
+                "apply_patch_freeform" => {
+                    continue;
+                }
                 "image_detail_original" => {
                     continue;
                 }
@@ -465,7 +467,6 @@ impl Features {
 
         for source in [base, profile] {
             LegacyFeatureToggles {
-                include_apply_patch_tool: source.include_apply_patch_tool,
                 experimental_use_unified_exec_tool: source.experimental_use_unified_exec_tool,
             }
             .apply(&mut features);
@@ -822,8 +823,8 @@ pub const FEATURES: &[FeatureSpec] = &[
     FeatureSpec {
         id: Feature::ApplyPatchFreeform,
         key: "apply_patch_freeform",
-        stage: Stage::Stable,
-        default_enabled: true,
+        stage: Stage::Removed,
+        default_enabled: false,
     },
     FeatureSpec {
         id: Feature::ApplyPatchStreamingEvents,
diff --git a/codex-rs/features/src/tests.rs b/codex-rs/features/src/tests.rs
index 21a6ecf5bab7..bd55ef8e7dbc 100644
--- a/codex-rs/features/src/tests.rs
+++ b/codex-rs/features/src/tests.rs
@@ -66,6 +66,16 @@ fn image_detail_original_is_removed_and_disabled_by_default() {
     assert_eq!(Feature::ImageDetailOriginal.default_enabled(), false);
 }
 
+#[test]
+fn apply_patch_freeform_is_removed_and_disabled_by_default() {
+    assert_eq!(Feature::ApplyPatchFreeform.stage(), Stage::Removed);
+    assert_eq!(Feature::ApplyPatchFreeform.default_enabled(), false);
+    assert_eq!(
+        feature_for_key("apply_patch_freeform"),
+        Some(Feature::ApplyPatchFreeform)
+    );
+}
+
 #[test]
 fn code_mode_only_requires_code_mode() {
     let mut features = Features::with_defaults();
@@ -403,7 +413,6 @@ fn from_sources_applies_base_profile_and_overrides() {
         },
         FeatureConfigSource {
             features: Some(&profile_features),
-            include_apply_patch_tool: Some(true),
             ..Default::default()
         },
         FeatureOverrides {
@@ -414,7 +423,7 @@ fn from_sources_applies_base_profile_and_overrides() {
     assert_eq!(features.enabled(Feature::Plugins), true);
     assert_eq!(features.enabled(Feature::CodeModeOnly), true);
     assert_eq!(features.enabled(Feature::CodeMode), true);
-    assert_eq!(features.enabled(Feature::ApplyPatchFreeform), true);
+    assert_eq!(features.enabled(Feature::ApplyPatchFreeform), false);
     assert_eq!(features.enabled(Feature::WebSearchRequest), false);
 }
 
@@ -472,6 +481,23 @@ fn from_sources_ignores_removed_js_repl_feature_keys() {
     assert_eq!(features, Features::with_defaults());
 }
 
+#[test]
+fn from_sources_ignores_removed_apply_patch_freeform_feature_key() {
+    let features_toml =
+        FeaturesToml::from(BTreeMap::from([("apply_patch_freeform".to_string(), true)]));
+
+    let features = Features::from_sources(
+        FeatureConfigSource {
+            features: Some(&features_toml),
+            ..Default::default()
+        },
+        FeatureConfigSource::default(),
+        FeatureOverrides::default(),
+    );
+
+    assert_eq!(features, Features::with_defaults());
+}
+
 #[test]
 fn multi_agent_v2_feature_config_deserializes_boolean_toggle() {
     let features: FeaturesToml = toml::from_str(
@@ -587,14 +613,13 @@ fn materialize_resolved_enabled_writes_all_features_and_preserves_custom_config(
             proxy_url: Some("http://127.0.0.1:43128".to_string()),
             ..Default::default()
         })),
-        entries: BTreeMap::from([("include_apply_patch_tool".to_string(), true)]),
+        entries: BTreeMap::new(),
         ..Default::default()
     };
 
     features_toml.materialize_resolved_enabled(&features);
 
     let entries = features_toml.entries();
-    assert_eq!(entries.get("include_apply_patch_tool"), None);
     for spec in crate::FEATURES {
         assert_eq!(
             entries.get(spec.key),
@@ -627,7 +652,7 @@ fn materialize_resolved_enabled_writes_all_features_and_preserves_custom_config(
         FeatureConfigSource::default(),
         FeatureOverrides::default(),
     );
-    assert_eq!(replayed.enabled(Feature::ApplyPatchFreeform), true);
+    assert_eq!(replayed.enabled(Feature::ApplyPatchFreeform), false);
 }
 
 #[test]
diff --git a/codex-rs/thread-manager-sample/src/main.rs b/codex-rs/thread-manager-sample/src/main.rs
index fff914eff3c3..a3a9adf26658 100644
--- a/codex-rs/thread-manager-sample/src/main.rs
+++ b/codex-rs/thread-manager-sample/src/main.rs
@@ -262,7 +262,6 @@ fn new_config(model: Option<String>, arg0_paths: Arg0DispatchPaths) -> anyhow::R
         experimental_thread_store: ThreadStoreConfig::Local,
         forced_chatgpt_workspace_id: None,
         forced_login_method: None,
-        include_apply_patch_tool: false,
         web_search_mode: Constrained::allow_any(WebSearchMode::Disabled),
         web_search_config: None,
         use_experimental_unified_exec_tool: false,
diff --git a/codex-rs/tools/src/tool_config.rs b/codex-rs/tools/src/tool_config.rs
index ad884e5be023..6e3ce1552629 100644
--- a/codex-rs/tools/src/tool_config.rs
+++ b/codex-rs/tools/src/tool_config.rs
@@ -175,7 +175,6 @@ impl ToolsConfig {
             session_source,
             ..
         } = params;
-        let include_apply_patch_tool = features.enabled(Feature::ApplyPatchFreeform);
         let include_code_mode = features.enabled(Feature::CodeMode);
         let include_code_mode_only = include_code_mode && features.enabled(Feature::CodeModeOnly);
         let include_goal_tools = features.enabled(Feature::Goals);
@@ -225,10 +224,7 @@ impl ToolsConfig {
             model_shell_type
         };
 
-        let apply_patch_tool_type = model_info
-            .apply_patch_tool_type
-            .clone()
-            .or_else(|| include_apply_patch_tool.then_some(ApplyPatchToolType::Freeform));
+        let apply_patch_tool_type = model_info.apply_patch_tool_type.clone();
 
         let agent_jobs_worker_tools = include_agent_jobs
             && matches!(
diff --git a/codex-rs/tools/src/tool_config_tests.rs b/codex-rs/tools/src/tool_config_tests.rs
index 252ad7a3205a..2fa49b03bf4d 100644
--- a/codex-rs/tools/src/tool_config_tests.rs
+++ b/codex-rs/tools/src/tool_config_tests.rs
@@ -4,7 +4,6 @@ use codex_features::Features;
 use codex_protocol::config_types::WebSearchMode;
 use codex_protocol::config_types::WindowsSandboxLevel;
 use codex_protocol::models::PermissionProfile;
-use codex_protocol::openai_models::ApplyPatchToolType;
 use codex_protocol::openai_models::ConfigShellToolType;
 use codex_protocol::openai_models::InputModality;
 use codex_protocol::openai_models::ModelInfo;
@@ -156,7 +155,7 @@ fn shell_zsh_fork_prefers_shell_command_over_unified_exec() {
 }
 
 #[test]
-fn fallback_apply_patch_models_use_freeform_tool_by_default() {
+fn fallback_apply_patch_models_do_not_use_freeform_tool_by_default() {
     let model_info = model_info();
     let features = Features::with_defaults();
 
@@ -172,10 +171,7 @@ fn fallback_apply_patch_models_use_freeform_tool_by_default() {
         windows_sandbox_level: WindowsSandboxLevel::Disabled,
     });
 
-    assert_eq!(
-        tools_config.apply_patch_tool_type,
-        Some(ApplyPatchToolType::Freeform)
-    );
+    assert_eq!(tools_config.apply_patch_tool_type, None);
 }
 
 #[test]