checkpoint: refresh remaining stale compact-transcript comments

Two leftover comments still described transcript.jsonl as pre-sliced / not referenced by metadata:

• paths.go CompactTranscriptFileName: now notes it holds the full compacted session, sliced at compact_transcript_start.
• persistent.go writeTranscript doc: it writes the full compacted session and returns the compactStart offset recorded as CompactTranscriptStart.

(attribution.go's "scoped to this checkpoint" refers to prompt.txt scoping, a separate and still-accurate concept, so it is left as-is.)