feat(copilot): warn before skills default rollout

[WOLIKIMCHENG]

Description

Adds a deprecation warning for Copilot's legacy markdown scaffold when users initialize Copilot without --skills.

This keeps the current .github/agents/*.agent.md + .github/prompts/ default behavior intact, while pointing users to opt in early with --integration-options "--skills" before skills mode becomes the default in a future release.

Scope of this change:

• keep Copilot markdown mode as the default
• warn when default Copilot setup uses the legacy markdown scaffold
• keep explicit Copilot --skills installs warning-free
• add direct setup and CLI init coverage for the warning behavior

Testing

• Tested locally with uv run specify --help
• Tested with a sample project (if applicable)

Focused validation run:

• .venv/bin/python -m pytest tests/integrations/test_integration_copilot.py -q
• .venv/bin/python -m pytest tests/integrations/test_cli.py -q
• .venv/bin/python -m pytest tests/integrations/test_integration_subcommand.py -q
• uvx ruff check src/specify_cli/integrations/copilot/__init__.py tests/integrations/test_integration_copilot.py
• git diff --check

All focused checks above passed locally.

[mnriem]

Thanks for tackling this, @WOLIKIMCHENG. Defaulting Copilot to skills mode is a reasonable long-term direction, but I'd like to push back on both the rollout and the justification.

1. Drop "Fixes #865" — this PR doesn't fix it.
Slash commands in Copilot do work; #865 isn't an actual defect in the markdown/.agent.md path, and nothing in this change addresses it. Please remove the Fixes #865 reference entirely (don't auto-close that issue on merge). The default flip needs to stand on its own merits, not on an unrelated, non-reproducing report.

2. The legacy mode becomes unreachable, not just non-default.
Flag options in _parse_integration_options (_helpers.py) can only ever be set to True when present — there's no negation, and IntegrationOption.default isn't seeded into parsed_options. Behavior is driven solely by parsed_options.get("skills", True) in setup(). After this change there's no CLI path that produces the .agent.md layout — it survives only because tests call setup(skills=False) directly. We don't want to remove that mode.

3. This needs a deprecation cycle.
Main is currently at 0.12.x (latest release v0.12.1). Proposed plan:

• Now (0.12/0.13): keep markdown as the default but emit a deprecation warning on Copilot init telling users skills mode is becoming the default and how to opt in early. There's precedent in this same file — see the SPECKIT_ALLOW_ALL_TOOLS deprecation warning.
• Flip the default 2 minor (Y) releases later (0.14.0), giving users a heads-up window.

So this PR shouldn't merge the flip yet — let's split it into "add deprecation warning now" and "flip default later."

4. Add an explicit --agents opt-out, and preserve existing users on flip.
When skills becomes the default, users need a way back to the legacy layout — please add --agents (negation support in the option parser) selecting the .github/agents/*.agent.md + .github/prompts/ + .vscode/settings.json scaffold. And the flip must respect .specify/init-options.json: markdown installs don't set ai_skills: true, so re-init/upgrade has to read and rewrite/normalize that file for existing --agents users so they aren't silently migrated onto skills.

[WOLIKIMCHENG]

Thanks for the detailed guidance. That makes sense.

I revised the PR to remove the default flip and keep the current markdown layout as the default. The PR now only adds a deprecation warning for default Copilot legacy markdown setup and points users to --integration-options "--skills" as the early opt-in path.

I also removed the Fixes #865 framing from the PR body. The default flip, explicit --agents opt-out, and .specify/init-options.json preservation/migration behavior can be handled in a later PR with the rollout window you described.

[Copilot]

Pull request overview

Adds a user-visible warning when Copilot is initialized in the legacy “.agent.md + .prompt.md” default mode, nudging users to opt into --skills ahead of an eventual default switch.

Changes:

• Emit a UserWarning during Copilot setup when --skills was not provided (legacy default path).
• Add direct integration-level tests verifying the warning behavior (warns in default mode, no warning in skills mode).
• Add CLI init tests verifying the same warning behavior through specify init.

Show a summary per file

File	Description
tests/integrations/test_integration_copilot.py	Adds unit + CLI coverage around the new deprecation warning behavior for default vs --skills Copilot setup.
src/specify_cli/integrations/copilot/init.py	Introduces _warn_legacy_markdown_default() and triggers it only for default (non-skills) Copilot scaffolding.

Review details

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• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Low

[mnriem]

Please address Copilot feedback

[WOLIKIMCHENG]

Addressed the Copilot feedback by changing the skills-mode warning assertion to check only that the legacy markdown deprecation warning is absent. The focused Copilot integration test file passes locally.