fix(cli,sdk): warn when squad.agent.md template is missing during upgrade/init

[diberry]

Closes #730

What

• upgrade.ts: Add warning when template source missing in version-current path
• init.ts: Track template-missing warning in structured return data (new \warnings\ field on \InitResult)
• Tests: Happy-path regression guard + missing-template warning test

Why

2 code paths silently skip squad.agent.md creation when the template source is missing. Users lose their coordinator instructions with no warning.

Changes

File	Change
\packages/squad-cli/src/cli/core/upgrade.ts\	Add \�lse { warn(...) }\ to version-current path
\packages/squad-sdk/src/config/init.ts\	Add \warnings: string[]\ to \InitResult, track missing template
\ est/cli/upgrade.test.ts\	Happy-path regression: verify squad.agent.md refreshed in version-current path
\ est/init-scaffolding.test.ts\	Happy-path + missing-template warning via proxy storage
.changeset/fix-silent-agent-md-skip.md\	Patch changeset for both packages

Working as EECOM (Core Dev)

[Copilot]

Pull request overview

This PR addresses a silent failure mode where .github/agents/squad.agent.md is not created/refreshed during squad init or squad upgrade when the squad.agent.md.template source is missing, by surfacing explicit warnings and adding regression tests.

Changes:

• CLI: warn in the upgrade “already current version” path when squad.agent.md.template is missing.
• SDK: extend InitResult with a warnings array and record a warning when the agent template is missing during initSquad.
• Tests: add regression coverage for the version-current upgrade refresh and init missing-template warning behavior.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
packages/squad-cli/src/cli/core/upgrade.ts	Adds a warning when the template is missing in the “already current” upgrade path.
packages/squad-sdk/src/config/init.ts	Adds warnings: string[] to InitResult and pushes a warning when the agent template is missing.
test/cli/upgrade.test.ts	Adds a regression test ensuring squad.agent.md is refreshed even when already current.
test/init-scaffolding.test.ts	Adds tests for happy-path creation and missing-template warning behavior in initSquad.
.changeset/fix-silent-agent-md-skip.md	Declares patch releases for CLI and SDK and describes the warning + new result field.

[tamirdresher]

Nice catch Dina. This is a real bug - users silently losing their coordinator instructions is bad. Clean fix, good tests.

One small thing: the PR description has a Unicode rendering glitch - \�lse { warn(...) } should be else { warn(...) }. Mind fixing the description text?

Other than that, LGTM. Merging this first.

Also did a quick compare with how microsoft/aspire handles similar stuff - they use a PR template with checkboxes but don't have automated validation like this. We're ahead here.

[tamirdresher]

Approved. Merge first in the batch.