[Checkpoints V2] Tag "thinking" lines for compact transcript

[computermode]

Adds "thinking..." tags to their corresponding message blocks in the compact transcript.

(Work in progress + this doesn't gate shipping checkpoints V2 and this information isn't consumed by the CLI or UI. It was requested internally.)

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Note

Medium Risk
Changes the normalized transcript.jsonl output by retaining assistant thinking content for claude-code and emitting Gemini thoughts as thinking blocks, which may affect any downstream consumers expecting thinking to be stripped or thinking-only assistant lines to be dropped.

Overview
Compact transcript output now preserves assistant “thinking” content. For claude-code JSONL compaction, thinking blocks are kept (while redacted_thinking remains dropped), which also means assistant messages containing only thinking are no longer filtered out.

Gemini compaction now includes thoughts. Gemini messages’ thoughts[] are converted into {"type":"thinking","thinking":"..."} blocks and prepended to assistant content; tests and fixtures are updated accordingly.

^{Reviewed by Cursor Bugbot for commit 46c8809. Configure here.}

[Copilot]

Pull request overview

This PR updates the compact transcript generator to include explicit thinking blocks (and Gemini thoughts) in the emitted content arrays, so “thinking” can be associated with the surrounding assistant message blocks in the compact JSONL format.

Changes:

• Preserve Claude Code thinking blocks (while still dropping redacted_thinking) during compacting.
• Emit Gemini thoughts as {"type":"thinking","thinking":"..."} blocks in compact output (including thought-only assistant messages).
• Update compact transcript fixtures and unit tests to expect the new thinking blocks.

Reviewed changes

Copilot reviewed 6 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
cmd/entire/cli/transcript/compact/compact.go	Adds a preserve-thinking path for Claude Code and updates assistant-content stripping to keep thinking blocks.
cmd/entire/cli/transcript/compact/compact_test.go	Adjusts compact tests to expect preserved thinking blocks (including thinking-only assistant).
cmd/entire/cli/transcript/compact/gemini.go	Adds Gemini thoughts parsing and emits them as thinking blocks in compact transcripts.
cmd/entire/cli/transcript/compact/gemini_test.go	Adds test coverage for a Gemini assistant message with only thoughts (no content/tool calls).
cmd/entire/cli/transcript/compact/testdata/claude_expected.jsonl	Updates expected Claude fixture output to include a thinking block.
cmd/entire/cli/transcript/compact/testdata/claude_expected2.jsonl	Updates expected Claude fixture output to include thinking blocks (including empty thinking markers).
cmd/entire/cli/transcript/compact/testdata/gemini_expected.jsonl	Updates expected Gemini fixture output to include thought-derived thinking blocks.