Problem

After PR #9159 added native tool support, users experienced a false 'tool has already been used in this message' error on every turn when using XML protocol (default).

Root Cause

In Task.ts, when the stream completes, the code was unconditionally merging parsed content blocks with native tool blocks:

const nativeToolBlocks = this.assistantMessageContent.filter((block) => block.type === 'tool_use')
const parsedBlocks = this.assistantMessageParser.getContentBlocks()
this.assistantMessageContent = [...parsedBlocks, ...nativeToolBlocks]

For XML protocol, parsedBlocks already contained the tool_use blocks parsed from XML text. The merge duplicated them - adding the same tool twice. When the first tool executed and set didAlreadyUseTool = true, the duplicate was incorrectly blocked.

Solution

Added protocol detection to only merge native tool blocks when using native protocol:

if (isNativeProtocol(toolProtocol)) {
    // Native protocol: merge parsed text with native tool blocks (have IDs)
    const nativeToolBlocks = this.assistantMessageContent.filter(
        (block): block is ToolUse<any> => block.type === 'tool_use' && (block as any).id !== undefined
    )
    this.assistantMessageContent = [...parsedBlocks, ...nativeToolBlocks]
} else {
    // XML protocol: use only parsed blocks (no merging needed)
    this.assistantMessageContent = parsedBlocks
}

Also fixed the approval feedback flow to avoid prematurely setting the didAlreadyUseTool flag.

Testing

• All existing tests pass
• TypeScript compilation successful
• Manually verified fix resolves the issue