fix: use thinking content in encode_conversations_with_harmony

[yurekami]

Summary

• Fixes encode_conversations_with_harmony to properly use message["thinking"] instead of message["content"] when the "thinking" key is present
• Also includes the final content with "final" channel when both thinking and content are present
• Previously, the thinking/analysis content was completely lost

Related Issue

Fixes #246

Test plan

• Verify messages with thinking key now properly encode the thinking content with "analysis" channel
• Verify messages with both thinking and content include both pieces of content
• Verify messages without thinking still work as expected

🤖 Generated with Claude Code

[gemini-code-assist]

Summary of Changes

Hello @yurekami, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request resolves an issue within the encode_conversations_with_harmony function that previously led to the omission of critical 'thinking' content from assistant messages. The updated logic ensures that when an assistant message includes a 'thinking' key, its content is properly captured and channeled as 'analysis'. Furthermore, if a 'content' key is also present, it is now explicitly included as 'final' content, thereby preserving the full context of the assistant's response and preventing data loss.

Highlights

• Corrected Thinking Content Usage: The encode_conversations_with_harmony function now correctly uses message["thinking"] for assistant messages when the 'thinking' key is present, ensuring this analytical content is not lost.
• Inclusion of Final Content: When both 'thinking' and 'content' keys are present in an assistant message, the final content is now also included with a 'final' channel, providing a complete conversation record.
• Bug Fix: This pull request fixes a bug where the 'thinking' or analysis content from assistant messages was previously completely lost during conversation encoding.

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[gemini-code-assist]

Code Review

This pull request correctly fixes an issue where thinking content in assistant messages was being ignored. The new logic properly encodes thinking content as an 'analysis' message and, if present, also includes the content as a 'final' message. My review includes a suggestion to ensure consistency by checking that thinking content is not empty before processing, similar to how content is handled. This will prevent the creation of empty 'analysis' messages.

[gemini-code-assist]

For consistency with how message["content"] is handled within this block (line 1353), you should also check if message["thinking"] is not empty before creating a message from it. This will prevent creating empty 'analysis' messages and makes the logic more robust.

Suggested change

	if "thinking" in message:
	if "thinking" in message and message["thinking"]: