fix: refresh speckit_version in init-options on integration update

[PascalThuet]

Summary

• Refresh .specify/init-options.json speckit_version whenever active integration metadata is updated.
• Refresh the same version field for multi-agent install/upgrade paths without changing the default integration fields.
• Add regression tests for default and non-default integration update paths.

Why

init-options.json stores active integration metadata such as integration, ai, context_file, script, and ai_skills, but speckit_version stayed pinned to the version that originally initialized the project.

After upgrading Spec Kit, that made init-options.json diverge from .specify/integration.json and the integration manifests, which already record the current Spec Kit version.

For multi-agent projects, non-default integration installs/upgrades also update .specify/integration.json, so this keeps the global init-options version aligned while preserving the active ai, integration, and context_file values.

If the intended meaning of this field is historical instead, it should probably be renamed or documented separately, for example as initialized_speckit_version.

Validation

• uv run pytest tests/integrations/test_integration_subcommand.py -v

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Adds tracking of the current speckit_version in .specify/init-options.json and ensures integration upgrade refreshes it.

Changes:

• Persist speckit_version when updating integration init options.
• Add an integration test verifying integration upgrade --force updates speckit_version.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
tests/integrations/test_integration_subcommand.py	Adds test coverage to ensure speckit_version is refreshed during upgrade.
src/specify_cli/init.py	Writes the current speckit_version into init options during integration option updates.

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