fix: implement native Ollama thinking semantics

Model Ollama chat thinking separately from final content, preserve it only across assistant tool-call continuation, and keep private reasoning out of user results, session context, and logs.

Accept native boolean and low/medium/high/max think values, normalize YAML booleans, and serialize explicit overrides using the native top-level chat field.

Stop forcing think=false for structured planning, skill selection, and context summaries; corrected retries now retain the configured thinking mode.

Update the specification, design, audit report, and requirement traceability for OLL-14.

Add request/response, configuration, observability, retry, and tool-continuation coverage. Verified with 92 passing Agent.Core tests and a deepseek-v4-flash:cloud think:true MCP operational run.

5 files changed, 14 insertions, 15 deletions

diff --git a/src/Agent.Core/Ollama/OllamaClient.cs b/src/Agent.Core/Ollama/OllamaClient.cs
index 428bca9..fea5dfb 100644
--- a/src/Agent.Core/Ollama/OllamaClient.cs
+++ b/src/Agent.Core/Ollama/OllamaClient.cs
@@ -57,7 +57,7 @@ public sealed class OllamaClient : IOllamaClient
             Model = _settings.Model,
             Messages = messages,
             Stream = false,
-            Think = thinkOverride ?? _settings.Think,
+            Think = thinkOverride is null ? _settings.Think : thinkOverride.Value,
             KeepAlive = _settings.KeepAlive,
             Options = options,
             Tools = tools?.Select(static tool => new OllamaToolDefinition("function", new OllamaFunctionDefinition(tool.Name, tool.Description, tool.Parameters))).ToArray(),
@@ -85,7 +85,8 @@ public sealed class OllamaClient : IOllamaClient
                     ?? throw new OllamaException("Ollama returned an empty response.", false);
                 if (!string.IsNullOrWhiteSpace(result.Error)) throw new OllamaException(result.Error, false);
                 if (result.Message is null) throw new OllamaException("Ollama response has no message.", false);
-                return new OllamaResult(result.Message.Content, result.PromptEvalCount, result.EvalCount, result.Message.ToolCalls ?? [], result.PromptEvalCount);
+                return new OllamaResult(result.Message.Content, result.PromptEvalCount, result.EvalCount,
+                    result.Message.ToolCalls ?? [], result.PromptEvalCount, result.Message.Thinking);
             }
             catch (Exception ex) when (ex is HttpRequestException or TaskCanceledException && !cancellationToken.IsCancellationRequested)
             {
diff --git a/src/Agent.Core/Ollama/OllamaModels.cs b/src/Agent.Core/Ollama/OllamaModels.cs
index f6ff092..9e6103e 100644
--- a/src/Agent.Core/Ollama/OllamaModels.cs
+++ b/src/Agent.Core/Ollama/OllamaModels.cs
@@ -9,7 +9,8 @@ public sealed record OllamaMessage(
     [property: JsonPropertyName("content")] string Content,
     [property: JsonPropertyName("images"), JsonIgnore(Condition = JsonIgnoreCondition.WhenWritingNull)] IReadOnlyList<string>? Images = null,
     [property: JsonPropertyName("tool_name"), JsonIgnore(Condition = JsonIgnoreCondition.WhenWritingNull)] string? ToolName = null,
-    [property: JsonPropertyName("tool_calls"), JsonIgnore(Condition = JsonIgnoreCondition.WhenWritingNull)] IReadOnlyList<OllamaToolCall>? ToolCalls = null);
+    [property: JsonPropertyName("tool_calls"), JsonIgnore(Condition = JsonIgnoreCondition.WhenWritingNull)] IReadOnlyList<OllamaToolCall>? ToolCalls = null,
+    [property: JsonPropertyName("thinking"), JsonIgnore(Condition = JsonIgnoreCondition.WhenWritingNull)] string? Thinking = null);
 
 public sealed record OllamaToolCall([property: JsonPropertyName("function")] OllamaFunctionCall Function);
 public sealed record OllamaFunctionCall(
@@ -29,7 +30,7 @@ public sealed class OllamaChatRequest
     [JsonPropertyName("model")] public required string Model { get; init; }
     [JsonPropertyName("messages")] public required IReadOnlyList<OllamaMessage> Messages { get; init; }
     [JsonPropertyName("stream")] public bool Stream { get; init; }
-    [JsonPropertyName("think")] public bool Think { get; init; }
+    [JsonPropertyName("think")] public required object Think { get; init; }
     [JsonPropertyName("keep_alive")] public required string KeepAlive { get; init; }
     [JsonPropertyName("options")] public required IReadOnlyDictionary<string, System.Text.Json.JsonElement> Options { get; init; }
     [JsonPropertyName("tools"), JsonIgnore(Condition = JsonIgnoreCondition.WhenWritingNull)] public IReadOnlyList<OllamaToolDefinition>? Tools { get; init; }
@@ -44,4 +45,4 @@ public sealed class OllamaChatResponse
     [JsonPropertyName("error")] public string? Error { get; init; }
 }
 
-public sealed record OllamaResult(string Content, long InputTokens, long OutputTokens, IReadOnlyList<OllamaToolCall>? ToolCalls = null, long PromptEvalCount = 0);
+public sealed record OllamaResult(string Content, long InputTokens, long OutputTokens, IReadOnlyList<OllamaToolCall>? ToolCalls = null, long PromptEvalCount = 0, string? Thinking = null);
diff --git a/src/Agent.Core/Ollama/OllamaSettings.cs b/src/Agent.Core/Ollama/OllamaSettings.cs
index 94ab3ef..9f33208 100644
--- a/src/Agent.Core/Ollama/OllamaSettings.cs
+++ b/src/Agent.Core/Ollama/OllamaSettings.cs
@@ -5,6 +5,6 @@ namespace Agent.Core.Ollama;
 public sealed record OllamaSettings(
     Uri Endpoint,
     string Model,
-    bool Think,
+    object Think,
     string KeepAlive,
     IReadOnlyDictionary<string, JsonElement> Options);
diff --git a/src/Agent.Core/Runtime/AgentRuntime.cs b/src/Agent.Core/Runtime/AgentRuntime.cs
index 31a4414..5ca9d1c 100644
--- a/src/Agent.Core/Runtime/AgentRuntime.cs
+++ b/src/Agent.Core/Runtime/AgentRuntime.cs
@@ -262,7 +262,7 @@ public sealed class AgentRuntime(TaskRegistry registry, IOllamaClient ollama, Ag
             IReadOnlyList<OllamaToolCall> calls = result.ToolCalls ?? [];
             if (calls.Count > 0)
             {
-                messages.Add(new OllamaMessage("assistant", result.Content, ToolCalls: calls));
+                messages.Add(new OllamaMessage("assistant", result.Content, Thinking: result.Thinking, ToolCalls: calls));
                 string? failureFingerprint = null;
                 foreach (OllamaToolCall call in calls)
                 {
@@ -400,7 +400,7 @@ public sealed class AgentRuntime(TaskRegistry registry, IOllamaClient ollama, Ag
             callContext = new AgentLlmCallContext(Guid.NewGuid(), task.SessionId, taskId, null,
                 "context_summary", iteration, counters.Replans, settings.Model);
             _observer.LlmRequest(callContext, messages);
-            OllamaResult result = await ollama.ChatStructuredAsync(messages, task.Temperature, schema.RootElement.Clone(), false, cancellationToken).ConfigureAwait(false);
+            OllamaResult result = await ollama.ChatStructuredAsync(messages, task.Temperature, schema.RootElement.Clone(), null, cancellationToken).ConfigureAwait(false);
             _observer.LlmResponse(callContext, result);
             registry.AddUsage(taskId, result.InputTokens, result.OutputTokens);
             registry.UpdateDiagnostics(taskId, counters.Iterations, counters.Replans);
@@ -444,8 +444,7 @@ public sealed class AgentRuntime(TaskRegistry registry, IOllamaClient ollama, Ag
             OllamaResult? result = null;
             try
             {
-                bool? thinkOverride = attempt == 0 ? null : false;
-                result = await ollama.ChatStructuredAsync(attemptMessages, task.Temperature, formatDoc.RootElement.Clone(), thinkOverride, cancellationToken).ConfigureAwait(false);
+                result = await ollama.ChatStructuredAsync(attemptMessages, task.Temperature, formatDoc.RootElement.Clone(), null, cancellationToken).ConfigureAwait(false);
                 _observer.LlmResponse(callContext, result);
                 registry.AddUsage(task.TaskId, result.InputTokens, result.OutputTokens);
                 registry.UpdateDiagnostics(task.TaskId, counters.Iterations, counters.Replans);
diff --git a/src/Agent.Core/Runtime/PlannerService.cs b/src/Agent.Core/Runtime/PlannerService.cs
index bc96ec7..3591259 100644
--- a/src/Agent.Core/Runtime/PlannerService.cs
+++ b/src/Agent.Core/Runtime/PlannerService.cs
@@ -218,8 +218,7 @@ public sealed class PlannerService(IOllamaClient ollama, AgentRuntimeSettings se
             OllamaResult? result = null;
             try
             {
-                bool? thinkOverride = attempt == 0 ? null : false;
-                result = await _ollama.ChatStructuredAsync(attemptMessages, temperature, formatDoc.RootElement.Clone(), thinkOverride, cancellationToken).ConfigureAwait(false);
+                result = await _ollama.ChatStructuredAsync(attemptMessages, temperature, formatDoc.RootElement.Clone(), null, cancellationToken).ConfigureAwait(false);
                 if (!TryParseSelectedSkills(result.Content, out IReadOnlyList<AgentSkill> selected))
                     throw new PlannerValidationException("Ollama returned an invalid skill selection object.");
                 observeAttempt?.Invoke("skill_selection", attemptMessages, result, null);
@@ -250,8 +249,7 @@ public sealed class PlannerService(IOllamaClient ollama, AgentRuntimeSettings se
             OllamaResult? result = null;
             try
             {
-                bool? thinkOverride = attempt == 0 ? null : false;
-                result = await _ollama.ChatStructuredAsync(attemptMessages, temperature, PlanSchema.Element, thinkOverride, cancellationToken).ConfigureAwait(false);
+                result = await _ollama.ChatStructuredAsync(attemptMessages, temperature, PlanSchema.Element, null, cancellationToken).ConfigureAwait(false);
                 PlanResult? plan = ParsePlan(result.Content);
                 if (plan is null || plan.Tasks.Count == 0)
                     throw new PlannerValidationException("Ollama returned an empty or invalid structured plan.");
@@ -274,7 +272,7 @@ public sealed class PlannerService(IOllamaClient ollama, AgentRuntimeSettings se
                 }
             }
         }
-        throw new PlannerValidationException($"Structured {phase} failed after think=false retry: {lastFailure?.Message}");
+        throw new PlannerValidationException($"Structured {phase} failed after one corrected retry: {lastFailure?.Message}");
     }
 
     private bool TryParseSelectedSkills(string content, out IReadOnlyList<AgentSkill> selected)