diff --git a/backend/src/models/runtime-model-catalog.ts b/backend/src/models/runtime-model-catalog.ts
index fa28ebb0..e77c0e05 100644
--- a/backend/src/models/runtime-model-catalog.ts
+++ b/backend/src/models/runtime-model-catalog.ts
@@ -41,8 +41,11 @@ const runtimeModelSchema = z.object({
       supportsReasoningEffort: z.boolean(),
       supportsStore: z.boolean(),
       maxTokensField: z.string().optional(),
+      thinkingFormat: z.enum(["qwen", "qwen-chat-template"]).optional(),
     }).strict().optional(),
-  }).strict().optional(),
+  }).strict().refine((session) => !session.compatibility?.thinkingFormat || session.reasoning, {
+    message: "thinkingFormat requires reasoning: true",
+  }).optional(),
   metadataGeneration: z.object({ disableThinking: z.boolean() }).strict().optional(),
 }).strict();
 
diff --git a/backend/test/metadata-generation-models.test.ts b/backend/test/metadata-generation-models.test.ts
index 6f5d00b0..f1288350 100644
--- a/backend/test/metadata-generation-models.test.ts
+++ b/backend/test/metadata-generation-models.test.ts
@@ -95,6 +95,35 @@ test("returns empty catalogs when no runtime projection is configured", () => {
   expect(loadMetadataGenerationModels({}).catalog()).toEqual({ models: [], default: null });
 });
 
+test.each([
+  ["qwen-chat-template", true, true],
+  ["qwen", true, true],
+  ["qwen-typo", true, false],
+  ["qwen-chat-template", false, false],
+])("validates Qwen thinking format %s with reasoning=%s", (thinkingFormat, reasoning, valid) => {
+  const { catalogFile } = runtimeCatalog({
+    defaultInteraction: "local/qwen",
+    models: [{
+      id: "local/qwen", provider: "local", model: "qwen", label: "Qwen",
+      upstreamModel: "qwen", endpoint: { baseUrl: "http://localhost:8000/v1" },
+      authentication: { mode: "none" }, sessionAdapter: { mode: "openai_compatible" },
+      session: {
+        reasoning, contextWindow: 32768, maxTokens: 8192,
+        compatibility: {
+          supportsDeveloperRole: false, supportsReasoningEffort: false,
+          supportsStore: false, maxTokensField: "max_tokens", thinkingFormat,
+        },
+      },
+    }],
+  });
+  if (valid) {
+    expect(loadRuntimeModelCatalog(catalogFile).sessionModels()[0].session?.compatibility)
+      .toMatchObject({ thinkingFormat });
+  } else {
+    expect(() => loadRuntimeModelCatalog(catalogFile)).toThrow("runtime model catalog is invalid");
+  }
+});
+
 test("rejects a drifted default and an unprotected projection", () => {
   const drifted = runtimeCatalog({ defaultInteraction: "zai/missing" });
   expect(() => loadRuntimeModelCatalog(drifted.catalogFile)).toThrow("interaction default is invalid");
diff --git a/docs/general/pi-configuration.md b/docs/general/pi-configuration.md
index 9db489af..bb33c5a2 100644
--- a/docs/general/pi-configuration.md
+++ b/docs/general/pi-configuration.md
@@ -128,6 +128,51 @@ endpoint expects a model name different from the catalog key.
 Provider integrations remain declarative. Do not register providers from
 `harness/.pi/extensions/`; those extensions implement the workflow and human gates only.
 
+### Qwen 3.6 sessions and thinking controls
+
+For Qwen served through a vLLM-compatible chat template, declare the following inside the
+model's `session` block, alongside its context and output limits:
+
+```yaml
+reasoning: true
+compatibility:
+  supportsDeveloperRole: false
+  supportsReasoningEffort: false
+  supportsStore: false
+  maxTokensField: max_tokens
+  thinkingFormat: qwen-chat-template
+```
+
+This makes Pi send `chat_template_kwargs.enable_thinking` from the selected thinking level,
+with `preserve_thinking: true`. Choose **off** to explicitly disable thinking. The alternative
+`thinkingFormat: qwen` is for endpoints expecting top-level `enable_thinking`. Both formats
+require `reasoning: true`; declaring `reasoning: false` does not tell the server to disable
+thinking. Omit `thinkingFormat` to preserve Pi's default behavior for other providers.
+
+Regenerate projections with the updated host CLI and recreate the local core container after
+rebuilding it. Do not add these fields directly to generated Pi files. These controls do not
+force tool calls or certify the workflow; perform the operator verification above.
+
+```sh
+tht --installation /absolute/path/thothii-installation.yaml installation generate
+```
+
+Use the model identifier exposed by your endpoint, such as `qwen3.6-35b-a3b`, and limits
+supported by that deployment. The thinking format configures the Pi session adapter;
+metadata generation continues to use its separate LiteLLM settings.
+
+If a session displays text such as `{"type":"bash","command":"tht session show … --json"}`
+and never opens a review widget, that text is not an executed tool call. A verified cause
+was the Evidence JSON extension being loaded into interactive sessions and forcing
+`response_format: {type: "json_object"}`. Upgrade to the core image containing the fix:
+the extension belongs in `.pi/evidence-extensions/` and is loaded explicitly only by
+Evidence authoring. It must not also remain in the automatically loaded `.pi/extensions/`
+directory. Regenerating model configuration alone does not remove an extension from an old image.
+
+After upgrading, reload the browser and resume the session. Verify that Pi executes
+`tht session show` and opens a review widget. This fix does not require changing the Qwen
+server, forcing every turn to call a tool, or teaching the model to print tool-call JSON.
+
 ## Authentication
 
 Every provider chooses one explicit mode:
diff --git a/docs/research/2026-09-21-pi-qwen-compatibility.md b/docs/research/2026-09-21-pi-qwen-compatibility.md
new file mode 100644
index 00000000..42db6742
--- /dev/null
+++ b/docs/research/2026-09-21-pi-qwen-compatibility.md
@@ -0,0 +1,57 @@
+# Qwen 3.6: session tool-call failure and correction
+
+Date: 2026-09-21. Verified runtime: Pi coding agent and Pi AI 0.80.3.
+
+## Cause and correction
+
+Interactive sessions returned text resembling a bash call and stopped before the
+first review widget. The Evidence-only extension `tht-evidence-json-mode.ts` lived
+under `.pi/extensions`, so Pi automatically loaded it into interactive sessions.
+Its `before_provider_request` hook imposed `response_format: {type: "json_object"}`
+and temperature zero on every request.
+
+Replaying the captured startup request, with all original hooks preserved, isolated
+the cause. With JSON response format, Qwen returned the command as text and finish
+reason `stop`. Removing only that field produced a native `bash` call and finish
+reason `tool_calls`. Both requests contained the same 15 tools and used High thinking.
+
+The extension now lives in `.pi/evidence-extensions` and is loaded explicitly by
+`PiEvidenceRestructurer`. Evidence retains JSON output. Interactive sessions retain
+native tool calls. No changes to the remote Qwen server were required.
+
+Earlier SDK probes replaced `session.agent.onPayload`, inadvertently bypassing the
+extension hooks. Their success did not reproduce the application path and did not
+establish a model or server fault.
+
+## Model configuration
+
+The installation catalog now accepts optional `session.compatibility.thinkingFormat`
+values `qwen` and `qwen-chat-template`, requiring `reasoning: true`. Go validation,
+the backend schema, and generated catalog/Pi projections preserve this setting.
+It controls thinking; it was not the cause or correction of the tool-call failure.
+
+For the verified endpoint, `qwen-chat-template` sends `enable_thinking` and
+`preserve_thinking` inside `chat_template_kwargs`. Selecting Off explicitly disables
+thinking. Declaring `reasoning: false` alone does not disable thinking on the server.
+See the [operator configuration](../general/pi-configuration.md#qwen-36-sessions-and-thinking-controls)
+and [Pi 0.80.3 model documentation](https://github.com/earendil-works/pi/blob/v0.80.3/packages/coding-agent/docs/models.md#openai-compatibility).
+
+## Validation and local delivery
+
+- Catalog and projection regression tests failed before the compatibility change,
+  then passed. Go config/modelprojection/CLI tests, 84 targeted backend tests,
+  TypeScript checking, and the strict documentation build passed.
+- The extension-isolation regression failed before relocation. All 46 Evidence
+  authoring/restructurer tests and Ruff checks on changed Python files passed.
+- The rebuilt local core image has digest
+  `sha256:9cd593d7362dcbefe177f1b9eb4b9ffdf3010ced7bd7efc8fc3fdcd288f24579`.
+  Core/frontend were recreated, healthy, and returned HTTP 200.
+- A real `pi --mode rpc --no-session` probe with Qwen and High thinking executed
+  `tht session show` successfully and reached the first clarification widget.
+  The probe allowed only that read and `reviewer_select`; it stopped without
+  submitting a human response or recording decisions. Its temporary configuration
+  referenced the mounted credential because the original runtime lease had expired.
+- The user subsequently confirmed that the application now works.
+
+This verifies recovery from the startup failure. It does not certify every workflow
+phase or the separate LiteLLM metadata-generation path.
diff --git a/harness/.pi/extensions/tht-evidence-json-mode.ts b/harness/.pi/evidence-extensions/tht-evidence-json-mode.ts
similarity index 69%
rename from harness/.pi/extensions/tht-evidence-json-mode.ts
rename to harness/.pi/evidence-extensions/tht-evidence-json-mode.ts
index f5cfa038..c680ff16 100644
--- a/harness/.pi/extensions/tht-evidence-json-mode.ts
+++ b/harness/.pi/evidence-extensions/tht-evidence-json-mode.ts
@@ -1,5 +1,8 @@
 import type { ExtensionAPI } from "@earendil-works/pi-coding-agent";
 
+// Loaded explicitly by PiEvidenceRestructurer. Keep outside .pi/extensions:
+// JSON-only output prevents interactive sessions from emitting native tool calls.
+
 export default function (pi: ExtensionAPI) {
 	pi.on("before_provider_request", (event) => {
 		if (typeof event.payload !== "object" || event.payload === null) {
diff --git a/harness/tests/test_evidence_pi_restructurer.py b/harness/tests/test_evidence_pi_restructurer.py
index feaae1a3..4d7f71c9 100644
--- a/harness/tests/test_evidence_pi_restructurer.py
+++ b/harness/tests/test_evidence_pi_restructurer.py
@@ -59,7 +59,7 @@ def test_pi_restructurer_uses_an_ephemeral_no_tools_invocation(tmp_path, monkeyp
     ]
     assert "--no-skills" in argv
     assert argv[argv.index("--extension") + 1].endswith(
-        "/extensions/tht-evidence-json-mode.ts"
+        "/evidence-extensions/tht-evidence-json-mode.ts"
     )
     assert "--system-prompt" in argv
     assert argv[argv.index("--system-prompt") + 1] == "Evidence-only system prompt"
@@ -120,7 +120,7 @@ def test_evidence_authoring_skill_is_loadable_and_declares_the_wire_schema():
 
 def test_evidence_authoring_json_mode_extension_only_rewrites_the_provider_payload():
     extension = (
-        Path(__file__).parents[1] / ".pi" / "extensions" / "tht-evidence-json-mode.ts"
+        Path(__file__).parents[1] / ".pi" / "evidence-extensions" / "tht-evidence-json-mode.ts"
     ).read_text(encoding="utf-8")
 
     assert 'pi.on("before_provider_request"' in extension
@@ -129,6 +129,19 @@ def test_evidence_authoring_json_mode_extension_only_rewrites_the_provider_paylo
     assert "registerTool" not in extension
 
 
+def test_evidence_json_mode_is_not_auto_loaded_into_interactive_sessions():
+    from tht.evidence.authoring import authoring_skill_path
+
+    skill_path = authoring_skill_path()
+    restructurer = PiEvidenceRestructurer("pi", skill_path)
+    extension_path = restructurer._json_mode_extension
+    auto_extensions = skill_path.parents[2] / "extensions"
+
+    assert extension_path.is_file()
+    assert not extension_path.is_relative_to(auto_extensions)
+    assert not (auto_extensions / extension_path.name).exists()
+
+
 @pytest.mark.parametrize("response", [_candidate(), [_candidate()]])
 def test_pi_restructurer_normalizes_bounded_candidate_envelopes(
     tmp_path, monkeypatch, response,
diff --git a/harness/tht/evidence/authoring.py b/harness/tht/evidence/authoring.py
index fedf1a1b..9ceb5692 100644
--- a/harness/tht/evidence/authoring.py
+++ b/harness/tht/evidence/authoring.py
@@ -209,7 +209,7 @@ class PiEvidenceRestructurer:
         self._pi_executable = pi_executable
         self._skill_path = skill_path
         self._json_mode_extension = (
-            skill_path.parents[2] / "extensions" / "tht-evidence-json-mode.ts"
+            skill_path.parents[2] / "evidence-extensions" / "tht-evidence-json-mode.ts"
         )
         self._timeout_seconds = timeout_seconds
 
diff --git a/tools/tht/internal/config/installation_model_catalog_test.go b/tools/tht/internal/config/installation_model_catalog_test.go
index b7f8dd49..b9a1601d 100644
--- a/tools/tht/internal/config/installation_model_catalog_test.go
+++ b/tools/tht/internal/config/installation_model_catalog_test.go
@@ -28,6 +28,38 @@ func TestLoadAcceptsInstallationModelCatalog(t *testing.T) {
 	}
 }
 
+func TestLoadQwenThinkingCompatibility(t *testing.T) {
+	for _, test := range []struct {
+		name, format string
+		reasoning    bool
+		wantError    bool
+	}{
+		{"vllm template", "qwen-chat-template", true, false},
+		{"top level Qwen", "qwen", true, false},
+		{"unknown format", "qwen-typo", true, true},
+		{"thinking disabled in model capabilities", "qwen-chat-template", false, true},
+	} {
+		t.Run(test.name, func(t *testing.T) {
+			path, _, _, _ := writeInstallation(t, "local")
+			reasoning := "false"
+			if test.reasoning {
+				reasoning = "true"
+			}
+			catalog := strings.Replace(validModelCatalogYAML(), "            contextWindow: 32768",
+				"            reasoning: "+reasoning+"\n            compatibility:\n              thinkingFormat: "+test.format+"\n            contextWindow: 32768", 1)
+			rewriteInstallationCatalog(t, path, catalog)
+			_, err := Load(path)
+			if test.wantError {
+				if err == nil || !strings.Contains(err.Error(), "thinkingFormat") {
+					t.Fatalf("Load() error = %v, want thinkingFormat error", err)
+				}
+			} else if err != nil {
+				t.Fatalf("Load() error = %v", err)
+			}
+		})
+	}
+}
+
 func TestLoadAcceptsSharedDeepSeekBuiltinWithBundleAuthentication(t *testing.T) {
 	path, _, envFile, _ := writeInstallation(t, "local")
 	catalog := strings.Replace(validModelCatalogYAML(), "interaction: zai/glm-5.3", "interaction: deepseek/deepseek-v4-pro", 1)
diff --git a/tools/tht/internal/config/model_catalog.go b/tools/tht/internal/config/model_catalog.go
index b1fbdb27..fb264fcc 100644
--- a/tools/tht/internal/config/model_catalog.go
+++ b/tools/tht/internal/config/model_catalog.go
@@ -90,6 +90,7 @@ type ModelCompatibility struct {
 	SupportsReasoningEffort bool   `yaml:"supportsReasoningEffort" json:"supportsReasoningEffort"`
 	SupportsStore           bool   `yaml:"supportsStore" json:"supportsStore"`
 	MaxTokensField          string `yaml:"maxTokensField" json:"maxTokensField,omitempty"`
+	ThinkingFormat          string `yaml:"thinkingFormat,omitempty" json:"thinkingFormat,omitempty"`
 }
 
 type SessionModel struct {
@@ -270,6 +271,15 @@ func validateCatalogProvider(id string, provider ModelProvider, hasSession, hasM
 				if model.Session != nil && (model.Session.ContextWindow <= 0 || model.Session.MaxTokens <= 0) {
 					return fmt.Errorf("modelCatalog model %q/%q requires contextWindow and maxTokens", id, modelID)
 				}
+				if model.Session != nil && model.Session.Compatibility != nil {
+					format := model.Session.Compatibility.ThinkingFormat
+					if format != "" && format != "qwen" && format != "qwen-chat-template" {
+						return fmt.Errorf("modelCatalog model %q/%q compatibility.thinkingFormat is invalid", id, modelID)
+					}
+					if format != "" && !model.Session.Reasoning {
+						return fmt.Errorf("modelCatalog model %q/%q compatibility.thinkingFormat requires reasoning: true", id, modelID)
+					}
+				}
 			}
 		}
 	} else if provider.Session != nil {
diff --git a/tools/tht/internal/modelprojection/projection_test.go b/tools/tht/internal/modelprojection/projection_test.go
index bc098095..7e5ca61b 100644
--- a/tools/tht/internal/modelprojection/projection_test.go
+++ b/tools/tht/internal/modelprojection/projection_test.go
@@ -97,6 +97,30 @@ func TestDeepSeekBuiltinAndMetadataShareCatalogIdentityAndSecretReference(t *tes
 	}
 }
 
+func TestQwenThinkingFormatSurvivesCatalogAndPiProjection(t *testing.T) {
+	i := projectionFixture(t)
+	model := i.ModelCatalog.Providers["local"].Models["qwen"]
+	if err := json.Unmarshal([]byte(`{"reasoning":true,"contextWindow":32768,"maxTokens":8192,"compatibility":{"supportsDeveloperRole":false,"supportsReasoningEffort":false,"supportsStore":false,"maxTokensField":"max_tokens","thinkingFormat":"qwen-chat-template"}}`), model.Session); err != nil {
+		t.Fatal(err)
+	}
+	files, err := Render(i)
+	if err != nil {
+		t.Fatal(err)
+	}
+	for _, path := range []string{CatalogFile, PiModelsFile} {
+		if !bytes.Contains(files[path], []byte(`"thinkingFormat": "qwen-chat-template"`)) {
+			t.Fatalf("%s dropped Qwen thinking compatibility", path)
+		}
+	}
+	var models piModels
+	if err := json.Unmarshal(files[PiModelsFile], &models); err != nil {
+		t.Fatal(err)
+	}
+	if !models.Providers["local"].Models[0].Reasoning {
+		t.Fatal("Pi must know the model supports explicit thinking control")
+	}
+}
+
 func TestProjectionKeepsSingleUseInventoryOutOfSharedPiSelection(t *testing.T) {
 	i := projectionFixture(t)
 	p := i.ModelCatalog.Providers["zai"]