fix(upgrade): loop-* skill copy doubles the skills/ path segment

[diazMelgarejo]

Summary

_new_loop_assets() in harness_manager/upgrade.py computes each new loop-* skill's destination as dst_skills / src.relative_to(src_agent). src.relative_to(src_agent) already starts with skills/ (src_agent is .agent/, not .agent/skills/), and dst_skills is already .agent/skills/ — so every genuinely-new loop-* skill lands at .agent/skills/skills/loop-x/SKILL.md instead of .agent/skills/loop-x/SKILL.md. Both upgrade --dry-run's own report and the real file copy are wrong.

This went unnoticed because the existing test coverage in tests/test_loop_integrations.py only ever pre-seeds loop-triage at the destination before calling upgrade() — so it exercises the "already exists, skip" branch and never the fresh-copy branch that actually builds the destination path.

Fix

dst_agent / src.relative_to(src_agent), matching the sibling non-loop skill-copy block earlier in the same function (_plan(), ~15 lines above), which already gets this right.

Tests

New: test_upgrade_copies_missing_loop_skills_to_the_correct_path — calls upgrade() against a fresh target with none of the loop-* skills pre-seeded, and asserts each lands at the correct (non-doubled) path.

Confirmed via git stash that this test fails on the old code (asserts the doubled path is absent) and passes on the fix.

python3 -m pytest tests/test_loop_integrations.py -v
# 5 passed

Note

Fix duplicate skills/ path segment when copying loop-* skill files during upgrade

In _new_loop_assets, the destination path for loop-* skill copy actions was built using dst_skills / src.relative_to(src_agent), which produced .agent/skills/skills/loop-*/.... The fix uses dst_agent / src.relative_to(src_agent) instead, targeting the correct .agent/skills/loop-*/... path. A new integration test in test_loop_integrations.py asserts the correct destination and confirms no .agent/skills/skills directory is created.

^{Macroscope summarized 312f132.}

[diazMelgarejo]

Related, independent PRs — no dependency on this one:

• fix(recall): exclude superseded lessons from lessons.jsonl retrieval #60 — recall.py excludes superseded lessons from lessons.jsonl retrieval
• fix(io): force UTF-8 on stdout/stderr and candidate writes #61 — UTF-8 stdout/stderr + candidate writes in learn.py
• fix(io): use a context manager in _lesson_already_appended #62 — context manager in _lesson_already_appended (stacked on fix(io): force UTF-8 on stdout/stderr and candidate writes #61's branch on the fork side, both target master)

This PR (the upgrade.py path-doubling fix) is unrelated in code but came out of the same review pass — surfaced while checking upgrade --dry-run's output for the other three.

cc @codejunkie99 — happy to answer questions on any of these, or squash/reorder however's easiest to review.