feat: add message normalization for Ollama model compatibility

[jackccrawford]

Pull Request: Message Normalization for Ollama Model Compatibility

Summary

This PR adds message normalization to handle model-specific formatting requirements when using Ollama's OpenAI-compatible endpoint with MCP (Model Context Protocol) tool calling.

Fixes: #9249

Problem

Certain Ollama models fail during MCP tool calling in the second turn (after tool execution) due to message formatting incompatibilities:

• Mistral/Ministral models: Reject system messages appearing after tool messages
  • Error: 400 Bad Request: Unexpected role 'system' after role 'tool'
• Gemma3 models: Reject tool_calls with unexpected 'index' field
  • Error: 400 Bad Request: Invalid 'tool_calls': unknown variant 'index'

Solution

Added a message normalization layer in streamChatResponse.ts that detects model family and applies appropriate fixes before sending to Ollama API:

1. For Mistral/Ministral: Reorders system messages before tool interactions
2. For Gemma3: Removes 'index' field from tool_calls structure

Changes

New Files

• extensions/cli/src/util/messageNormalizer.ts - Message normalization utility

Modified Files

• extensions/cli/src/stream/streamChatResponse.ts - Integration point for normalization

Testing

Tested with Continue CLI using multiple Ollama cloud models and MCP servers (reachy-mini, filesystem):

✅ Working Models (MCP Tool Calling Confirmed)

• DeepSeek V3.1 (671B Cloud)
• Qwen3 Coder (480B Cloud)
• Qwen3 VL (235B Cloud)
• Qwen3 Next (80B Cloud)
• Cogito 2.1 (671B Cloud)
• GLM 4.6 (Cloud)
• Minimax M2 (Cloud)
• Kimi K2 (1T Cloud)

❌ Known Limitation

• Gemma3 (27B Cloud) - index field added after normalization by OpenAI adapter layer
  • Issue occurs downstream of our normalization point
  • Not blocking - all priority models work

Test Procedure

1. Start Continue CLI with Ollama models configured
2. Switch between different models
3. Execute MCP tool calls (e.g., "use reachy-mini to express joy")
4. Verify both Turn 1 (tool call generation) and Turn 2 (tool result processing) complete successfully

Implementation Details

Message Normalization Logic:

export function normalizeMessagesForModel(
  messages: ChatCompletionMessageParam[],
  modelName: string,
): ChatCompletionMessageParam[] {
  const modelLower = modelName.toLowerCase();

  if (modelLower.includes("mistral")) {
    return normalizeForMistral(messages);
  } else if (modelLower.includes("gemma")) {
    return normalizeForGemma(messages);
  }

  return messages; // No normalization needed
}

Integration Point:

Applied after convertFromUnifiedHistoryWithSystemMessage but before chatCompletionStreamWithBackoff in streamChatResponse.ts (line 265).

Backward Compatibility

• ✅ No breaking changes
• ✅ Only affects Mistral/Gemma models
• ✅ All other models pass through unchanged
• ✅ No performance impact (simple string matching + array operations)

Future Work

• Monitor for additional model-specific quirks
• Consider upstreaming similar fixes to Ollama if patterns emerge
• Track Gemma3 index field issue for potential fix in OpenAI adapter layer

Checklist

• Code follows Continue.dev style guidelines
• Formatted with Prettier
• No new linting errors
• Tested with multiple models
• Documentation updated
• GitHub issue created (Ollama models (Mistral, Gemma) fail during MCP tool calling due to message formatting incompatibilities #9249)
• CLA signed (will sign when submitting)

Related Issues

• Fixes Ollama models (Mistral, Gemma) fail during MCP tool calling due to message formatting incompatibilities #9249

Screenshots/Logs

Before (Gemma3 error):

Error: 400 Bad Request: Invalid 'tool_calls': unknown variant 'index'

After (DeepSeek V3.1 working):

● show(thinking)
  ⎿ [{"type":"text","text":"Expressed: thinking"}]

● speak(This is fascinating! I'm now performing a thinking movement...)
  ⎿ [{"type":"text","text":"Spoke: This is fascinating!..."}]

Perfect! The thinking expression was performed while the message was spoken.

Additional Context

This fix enables robust MCP tool calling across a wide range of Ollama models, improving the developer experience when using Continue CLI with local LLMs.

---

Summary by cubic

Add Ollama-specific message normalization to fix MCP tool-calling (Mistral/Ministral system-before-tool; remove Gemma tool_calls index), and an ocean-bus SSE subscriber that queues DM events, formats them as prompts, and triggers processing when idle for autonomous handling in Continue CLI. Fixes #9249.

^{Written for commit a329265. Summary will update automatically on new commits.}

[continue]

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[github-actions]

All contributors have signed the CLA ✍️ ✅
_{Posted by the CLA Assistant Lite bot.}

[cubic-dev-ai]

3 issues found across 13 files

Prompt for AI agents (all issues)

Check if these issues are valid — if so, understand the root cause of each and fix them.


<file name="PR_SUBMISSION_GUIDE.md">

<violation number="1" location="PR_SUBMISSION_GUIDE.md:101">
P2: This file explicitly states it should NOT be included in the PR (see line 98). This appears to be internal documentation for the PR author that was accidentally committed. Consider removing this file from the PR.</violation>
</file>

<file name="extensions/cli/src/util/messageNormalizer.ts">

<violation number="1" location="extensions/cli/src/util/messageNormalizer.ts:30">
P1: Ministral models won&#39;t be normalized because `&quot;ministral&quot;.includes(&quot;mistral&quot;)` is `false`. The check needs to also match &#39;ministral&#39; explicitly.</violation>
</file>

<file name="SHIP_IDE_MODIFICATIONS.md">

<violation number="1" location="SHIP_IDE_MODIFICATIONS.md:125">
P2: Hardcoded machine-specific path in documentation. Replace with a relative path or placeholder like `&lt;project-root&gt;` or simply indicate the user should be in the repository root.</violation>
</file>

---

Since this is your first cubic review, here's how it works:

• cubic automatically reviews your code and comments on bugs and improvements
• Teach cubic by replying to its comments. cubic learns from your replies and gets better over time
• Ask questions if you need clarification on any suggestion

_{Reply to cubic to teach it or ask questions. Re-run a review with @cubic-dev-ai review this PR}

[cubic-dev-ai]

P2: This file explicitly states it should NOT be included in the PR (see line 98). This appears to be internal documentation for the PR author that was accidentally committed. Consider removing this file from the PR.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At PR_SUBMISSION_GUIDE.md, line 101:

<comment>This file explicitly states it should NOT be included in the PR (see line 98). This appears to be internal documentation for the PR author that was accidentally committed. Consider removing this file from the PR.</comment>

<file context>
@@ -0,0 +1,170 @@
+
+- `SHIP_IDE_MODIFICATIONS.md` (Ship-specific)
+- `PR_DOCUMENTATION.md` (just for reference)
+- `PR_SUBMISSION_GUIDE.md` (this file)
+- Package lock files (unless specifically needed)
+
</file context>

✅ Addressed in e62bada

[cubic-dev-ai]

P1: Ministral models won't be normalized because "ministral".includes("mistral") is false. The check needs to also match 'ministral' explicitly.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At extensions/cli/src/util/messageNormalizer.ts, line 30:

<comment>Ministral models won&#39;t be normalized because `&quot;ministral&quot;.includes(&quot;mistral&quot;)` is `false`. The check needs to also match &#39;ministral&#39; explicitly.</comment>

<file context>
@@ -0,0 +1,106 @@
+  const modelLower = modelName.toLowerCase();
+
+  // Detect model family and apply appropriate normalization
+  if (modelLower.includes(&quot;mistral&quot;)) {
+    return normalizeForMistral(messages);
+  } else if (modelLower.includes(&quot;gemma&quot;)) {
</file context>

✅ Addressed in e62bada

[cubic-dev-ai]

P2: Hardcoded machine-specific path in documentation. Replace with a relative path or placeholder like <project-root> or simply indicate the user should be in the repository root.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At SHIP_IDE_MODIFICATIONS.md, line 125:

<comment>Hardcoded machine-specific path in documentation. Replace with a relative path or placeholder like `&lt;project-root&gt;` or simply indicate the user should be in the repository root.</comment>

<file context>
@@ -0,0 +1,167 @@
+
+```bash
+# Install dependencies at root
+cd /Users/mars/Dev/ship-ide/continue
+npm install
+
</file context>

✅ Addressed in e62bada

[jackccrawford]

I have read the CLA Document and I hereby sign the CLA

[continue]

Documentation Updates

I've reviewed the changes in this PR and created a companion documentation PR to help users understand the new message normalization feature.

Documentation PR: #9254

The documentation updates include:

• Troubleshooting section for the Mistral/Gemma MCP tool calling errors
• Ollama guide updates explaining automatic message normalization
• Best practices for choosing models with MCP tool support
• Cross-references between troubleshooting and guide sections

The docs are scoped to user-facing information and use Mintlify components (Accordion, Info) for better readability. No code changes were made.

cc @continuedev/maintainers - Please review the documentation PR alongside this feature PR.

[continue]

Review Issues Fixed

I've addressed all the issues identified by the code review:

✅ P1 - Critical Bug: Ministral Model Detection

Issue: The code checked modelLower.includes("mistral") but "ministral" does NOT contain "mistral" as a substring, so Ministral models wouldn't be normalized.

Fix: Updated the check to explicitly match both:

if (modelLower.includes("mistral") || modelLower.includes("ministral")) {

✅ P2 - Internal Documentation Files

Issue: Three internal documentation files were accidentally included:

• PR_DOCUMENTATION.md
• PR_SUBMISSION_GUIDE.md (which explicitly said it shouldn't be included!)
• SHIP_IDE_MODIFICATIONS.md

Fix: Removed all three files from the PR. These were internal notes for the PR author.

Changes committed: c87d546

[jackccrawford]

I have read the CLA Document and I hereby sign the CLA

[continue]

Documentation Updates

I've created a clean documentation PR for this feature.

Documentation PR: #9257

The new PR is documentation-only and includes:

• Troubleshooting section for the Mistral/Gemma MCP tool calling errors
• Ollama guide updates explaining automatic message normalization
• Best practices for choosing models with MCP tool support
• Cross-references between troubleshooting and guide sections

The docs are scoped to user-facing information and use Mintlify components (Accordion, Info) for better readability. This PR should be merged after #9253 is merged.

---

Note: Closed PR #9254 and replaced it with #9257 because the original docs PR mistakenly included code changes from this feature branch.

[cubic-dev-ai]

3 issues found across 8 files (changes from recent commits).

Prompt for AI agents (all issues)

Check if these issues are valid — if so, understand the root cause of each and fix them.


<file name="extensions/cli/src/services/OceanBusService.ts">

<violation number="1" location="extensions/cli/src/services/OceanBusService.ts:90">
P1: Bug: When filtering by event types with `clear: true`, this clears ALL queued events instead of only removing the returned events. Events that don&#39;t match the filter will be lost. Consider only removing the events that are returned, or document this behavior clearly.</violation>
</file>

<file name="SHIP_INTEGRATION_ANALYSIS.md">

<violation number="1" location="SHIP_INTEGRATION_ANALYSIS.md:455">
P2: Invalid TypeScript syntax in example code. Named arguments in TypeScript must be passed as an object, not with Python-style `param: value` syntax. This should be `oceanService.explore(&quot;&quot;, { limit: 5 })` or `oceanService.explore(&quot;&quot;, 5)` depending on the intended function signature.</violation>
</file>

<file name="extensions/cli/src/services/index.ts">

<violation number="1" location="extensions/cli/src/services/index.ts:326">
P1: Environment variable `OCEAN_BUS_URL` is read but never used to configure the service. The `oceanBusService` is instantiated at module level with the default URL. Either pass the URL to the constructor at instantiation time, or create the service instance inside the registration callback.</violation>
</file>

_{Reply to cubic to teach it or ask questions. Re-run a review with @cubic-dev-ai review this PR}

[cubic-dev-ai]

P1: Bug: When filtering by event types with clear: true, this clears ALL queued events instead of only removing the returned events. Events that don't match the filter will be lost. Consider only removing the events that are returned, or document this behavior clearly.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At extensions/cli/src/services/OceanBusService.ts, line 90:

<comment>Bug: When filtering by event types with `clear: true`, this clears ALL queued events instead of only removing the returned events. Events that don&#39;t match the filter will be lost. Consider only removing the events that are returned, or document this behavior clearly.</comment>

<file context>
@@ -0,0 +1,246 @@
+    }
+
+    // Clear queue if requested
+    if (clear) {
+      this.state.eventQueue = [];
+    }
</file context>

[cubic-dev-ai]

P2: Invalid TypeScript syntax in example code. Named arguments in TypeScript must be passed as an object, not with Python-style param: value syntax. This should be oceanService.explore("", { limit: 5 }) or oceanService.explore("", 5) depending on the intended function signature.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At SHIP_INTEGRATION_ANALYSIS.md, line 455:

<comment>Invalid TypeScript syntax in example code. Named arguments in TypeScript must be passed as an object, not with Python-style `param: value` syntax. This should be `oceanService.explore(&quot;&quot;, { limit: 5 })` or `oceanService.explore(&quot;&quot;, 5)` depending on the intended function signature.</comment>

<file context>
@@ -0,0 +1,930 @@
+  );
+
+  if (oceanService) {
+    const recentMemories = await oceanService.explore(&quot;&quot;, limit: 5);
+    systemMessage += `\n\nRecent Ocean Memories:\n${formatMemories(recentMemories)}`;
+  }
</file context>

[cubic-dev-ai]

P1: Environment variable OCEAN_BUS_URL is read but never used to configure the service. The oceanBusService is instantiated at module level with the default URL. Either pass the URL to the constructor at instantiation time, or create the service instance inside the registration callback.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At extensions/cli/src/services/index.ts, line 326:

<comment>Environment variable `OCEAN_BUS_URL` is read but never used to configure the service. The `oceanBusService` is instantiated at module level with the default URL. Either pass the URL to the constructor at instantiation time, or create the service instance inside the registration callback.</comment>

<file context>
@@ -318,6 +320,20 @@ export async function initializeServices(initOptions: ServiceInitOptions = {}) {
+  serviceContainer.register(
+    SERVICE_NAMES.OCEAN_BUS,
+    async () =&gt; {
+      const oceanBusUrl = process.env.OCEAN_BUS_URL || &quot;http://localhost:8765&quot;;
+      await oceanBusService.start();
+      return {
</file context>

[cubic-dev-ai]

1 issue found across 2 files (changes from recent commits).

Prompt for AI agents (all issues)

Check if these issues are valid — if so, understand the root cause of each and fix them.


<file name="extensions/cli/src/ui/hooks/useChat.ts">

<violation number="1" location="extensions/cli/src/ui/hooks/useChat.ts:231">
P1: Stale closure: `isWaitingForResponse` and `isCompacting` are captured at effect setup time and won&#39;t reflect current state. The useEffect dependency array is `[assistant]` but uses these state variables. Consider adding `isWaitingForResponse`, `isCompacting`, and `handleUserMessage` to the dependency array to ensure the handler always checks current state.</violation>
</file>

_{Reply to cubic to teach it or ask questions. Re-run a review with @cubic-dev-ai review this PR}

[cubic-dev-ai]

P1: Stale closure: isWaitingForResponse and isCompacting are captured at effect setup time and won't reflect current state. The useEffect dependency array is [assistant] but uses these state variables. Consider adding isWaitingForResponse, isCompacting, and handleUserMessage to the dependency array to ensure the handler always checks current state.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At extensions/cli/src/ui/hooks/useChat.ts, line 231:

<comment>Stale closure: `isWaitingForResponse` and `isCompacting` are captured at effect setup time and won&#39;t reflect current state. The useEffect dependency array is `[assistant]` but uses these state variables. Consider adding `isWaitingForResponse`, `isCompacting`, and `handleUserMessage` to the dependency array to ensure the handler always checks current state.</comment>

<file context>
@@ -226,6 +226,16 @@ export function useChat({
       logger.info(&quot;Ocean-bus event queued for processing&quot;);
+
+      // If LLM is idle, trigger queue processing
+      if (!isWaitingForResponse &amp;&amp; !isCompacting) {
+        const queuedMessageData = messageQueue.getNextMessage();
+        if (queuedMessageData) {
</file context>