Why skill-tree writes state to two different paths

I built skill-tree to classify my own Claude Code sessions against Anthropic's AI Fluency Index — 11 behaviors measured across 9,830 conversations in their February 2026 study. The core loop is straightforward: analyze session history, assign one of seven archetype cards, pick a behavior I haven't touched as a growth quest for next session. The growth quest only works if it persists. In Claude Code, that's simple: write to ~/.skill-tree/ and it's there next session. Cowork broke this immediately