Fix Gemini transcript position tracking

[peyton-alt]

Note

Low Risk
Scoped to transcript parsing/counting and hook-side new-content detection; main risk is off-by-one/format-detection regressions for edge-case transcripts.

Overview
Fixes Gemini transcript handling in the manual-commit strategy by counting transcript position as message count (via geminicli.ParseTranscript) instead of treating the JSON blob as a single line, keeping CheckpointTranscriptStart and condensation offsets consistent.

Improves Gemini format detection to treat any JSON object with a messages field (even an empty array) as Gemini format, and updates new-content checks (countTranscriptLines) to use the same counting logic. Adds targeted tests covering Gemini/Claude counting behavior and the empty-messages detection case.

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[Copilot]

Pull request overview

Updates manual-commit strategy transcript accounting so Gemini session transcripts track “position” by message count (instead of treating the whole JSON file as a single line), aligning condensation and “new content” detection with GeminiCLIAgent.GetTranscriptPosition().

Changes:

• Count Gemini transcript progress using parsed messages length (message count), not “1 line”.
• Update countTranscriptLines to detect Gemini JSON transcripts and count messages.
• Add unit tests covering transcript line/message counting behavior.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
cmd/entire/cli/strategy/manual_commit_hooks.go	Counts Gemini transcripts by message count for “has new content” checks.
cmd/entire/cli/strategy/manual_commit_condensation.go	Records FullTranscriptLines as Gemini message count to keep condensation offsets consistent with Gemini’s transcript position semantics.
cmd/entire/cli/strategy/manual_commit_test.go	Adds tests for countTranscriptLines across Claude JSONL and Gemini JSON cases.

[cursor]

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