feature: track managed artifact lifecycle and clean obsolete paths on upgrade #2232

Problem

An upgraded Squad repository can retain artifacts from older layouts that a fresh squad init no longer creates. Stale skills or instructions can still be discovered and influence agent behavior, while the repository remains structurally different from a fresh install.

In one observed upgrade, the existing repository retained 21 folders and 24 tracked files under .copilot/skills, while a fresh init had no .copilot/skills directory. The installed upgrade migration only moves legacy skill names listed in TEMPLATE_MANIFEST; other entries are intentionally left behind to avoid deleting user content. This protects unknown files, but leaves old Squad artifacts and user-added skills indistinguishable in a deprecated location.

Expected behavior

Squad should track the lifecycle of artifacts it manages, rather than relying on filesystem comparisons or broad deletion. A machine-readable manifest could record each artifact's ownership, introduced version, canonical location, migration target, and retirement policy.

During squad upgrade, Squad should:

• Identify known Squad-managed artifacts that are obsolete, moved, or need refresh.
• Migrate managed content to the canonical location, verify the destination, then remove the old managed copy.
• Preserve unknown or user-owned content and report conflicts instead of guessing.
• Make --dry-run list planned moves, updates, and removals, with the reason for each.
• Converge idempotently, so repeated upgrades do not leave managed artifacts drifting between layouts.

Acceptance criteria

• A legacy-install fixture with versioned managed files upgrades to the current canonical layout without leaving obsolete managed copies.
• A fixture with unknown or user-owned files at a deprecated path preserves them and reports the unresolved content.
• A dry run reports every planned artifact action without changing files.
• Upgrade verifies successful migration before removing a managed source file.
• Re-running upgrade produces no further changes.

This is distinct from #2047, which covers stale .squad/templates/skills and workflow snapshots, and builds on the versioned layout manifest proposal in #670. #1126 covers a prior skills-path migration, but not lifecycle tracking and safe retirement of artifacts from older layouts.