skillopt-sleep: harvest checkpoint is keyed by project, so a second --source in the same project skips its unseen sessions #312

What happens

skillopt-sleep run stores one harvest checkpoint per project, whatever --source the run used. cycle.py reads state.last_harvest_for(project) before harvesting and calls state.set_last_harvest(project, started) after every stateful run (both the no-tasks branch and the normal end). So when one project is fed from several transcript sources, one night per source, every source after the first only sees sessions newer than the first run's start: its older, never-harvested sessions are skipped for good. Each source is a separate store with its own timestamps, so a single shared cursor cannot be right for all of them.

Repro (mock backend, isolated state, no model calls)

Version: main at 343db22, installed with uv tool install "skillopt @ git+https://github.com/microsoft/SkillOpt", Python 3.14, macOS. --claude-home points the state at a scratch dir; P is an empty scratch project.

T=$(mktemp -d); mkdir -p $T/.claude $T/proj
common="--project $T/proj --scope all --backend mock --claude-home $T/.claude --progress"
skillopt-sleep dry-run $common --source codex   # harvest done: sessions=60
skillopt-sleep run     $common --source cursor  # stateful; sets last_harvest[$T/proj]
skillopt-sleep dry-run $common --source codex   # harvest done: sessions=0

(Our Codex sessions are CLI rollouts, so we pass --codex-home pointing at a dir whose archived_sessions/ symlinks ~/.codex/sessions/**/rollout-*.jsonl; see #282.)

The second codex dry-run harvests nothing although no codex session was ever harvested: it inherited the cursor run's checkpoint.

Expected

Each source keeps its own checkpoint.

Suggested fix

Key last_harvest by f"{project}::{transcript_source}" and fall back to the bare project key when reading existing state, or accept several --source values in one run so one checkpoint covers them together.

Workaround we use

A wrapper keeps one cursor per source in its own file and writes it into state.json before each per-source run.