Bug: squad upgrade leaves shipped .squad/templates/skills and workflows stale

Summary

squad init seeds a complete .squad/templates snapshot, but squad upgrade does not refresh the existing repository's .squad/templates/skills or .squad/templates/workflows directories. An older repository upgraded to the current CLI can therefore report a current Squad version while still using obsolete template skills and workflows.

Reproduction

1. Start with an older Squad repository whose .squad/templates directory already exists.
2. Run squad upgrade (or squad upgrade --dry-run) using the current CLI.
3. Compare the repository's .squad/templates contents with a fresh squad init at the same CLI version.

Observed in:

• Legacy repository: E:\src\Repository\.squad
• Fresh current install used for comparison: C:\source\squad-new-install\.squad
• CLI/SDK version: 0.13.1

Observed behavior

• squad upgrade --dry-run reports 0.13.1 -> 0.13.1 and lists Squad-owned files, but does not include .squad/templates/skills/* or .squad/templates/workflows/*.
• The legacy tree has 32 template skills; the current tree has 53.
• 21 current template skill files are missing from the legacy tree, and 29 shared skill files have different content.
• All 11 shared .squad/templates/workflows/*.yml files differ.

Examples:

• .squad/templates/skills/model-selection/SKILL.md
  • Current: YAML frontmatter, current model defaults such as gpt-5.6-luna, and the current five-layer model resolution rules.
  • Legacy: no current frontmatter and older claude-* defaults.
• .squad/templates/skills/cross-squad/SKILL.md
  • Current: newer triggers and the product-vs-English “squad” disambiguation protocol.
  • Legacy: older, shorter protocol.
• .squad/templates/workflows/squad-ci.yml
  • Current: actions pinned to commit SHAs.
  • Legacy: floating @v4 action tags.

Expected behavior

When upgrading an existing repository, Squad-owned static template content should reach parity with what a fresh squad init would seed for the same CLI version, including:

• .squad/templates/skills/**
• .squad/templates/workflows/**

User-specific mutable state must remain preserved. In particular, the upgrade must not overwrite or delete team/project state such as agents, team.md, decisions, identity, logs, orchestration logs, memory, casting state, routing, ceremonies, or user configuration.

Likely root cause

The upgrade implementation appears to intentionally skip skills and workflows while refreshing .squad/templates, because their operational destinations are .github/skills and .github/workflows. This creates a semantic mismatch: init creates a complete .squad/templates snapshot, while upgrade leaves existing copies of those static templates behind.

Relevant implementation/source references:

• upgrade.ts template refresh
• upgrade.ts skill synchronization
• templates.ts ownership manifest
• init.ts template seeding

Proposed fix

If .squad/templates is intended to remain a current static snapshot, update squad upgrade to refresh Squad-owned files under .squad/templates/skills and .squad/templates/workflows, while preserving target-only files and all mutable state exclusions.

Add regression coverage that upgrades an existing .squad/templates directory and verifies:

1. model-selection/SKILL.md is refreshed.
2. Newly introduced skill directories are added.
3. Existing shared workflow files are refreshed.
4. User-specific state and target-only files are preserved.

This issue is related to #1436, but this report focuses specifically on upgrade parity and stale template contents.