Fix upgrade path and skill manifest drift#48
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Summary
agentic-stack upgradewith--dry-run/--yesto refresh skeleton-owned.agentinfrastructure while leaving adapter configs, user memory, candidates, and existing skill dirs aloneagentic-stack sync-manifestand run manifest sync during install/add when.agent/skillsexistsdoctorwarn for missing Claude hook command targets and unwired hook filesFixes #45
Fixes #46
Fixes #47
Test Plan
python3 -m pytest -qpython3 -m py_compile harness_manager/cli.py harness_manager/install.py harness_manager/doctor.py harness_manager/skill_manifest.py harness_manager/upgrade.pybash -n install.shruby -c Formula/agentic-stack.rbsync-manifest,upgrade --dry-run,upgrade --yespython3 test_tldraw_visual_memory.pypython3 test_claude_code_hook.py