[WOLIKIMCHENG]

Description

Honor integration switch --refresh-shared-infra for installed targets, including the current default, through the existing shared installer. This refreshes customized shared scripts, page templates, and .specify/.gitignore while preserving separate teardown consent and the current-default no-flag no-op.

Testing

• Real CLI matrix: 2 failed/10 passed before the fix; 12 passed afterward.
• 413 focused tests passed on Linux/Python 3.11; Ruff 0.15.0 and whitespace checks passed.
• Full suite: 15,879 passed, 591 skipped, 8 host-sensitive failures involving Git author configuration and root permissions. Native Windows/macOS and Markdownlint were not run locally.

Manual test results

Agent: Codex following the generated skill | OS/Shell: Linux/Bash

Command tested	Notes
/speckit-specify	After installed-target refresh, the generated Claude skill's Bash resolver ran and the spec, 16-item checklist, and feature state were completed. No hooks were registered.

AI Disclosure

• I did use AI assistance (described below)

AI disclosure: AI-assisted tools were used to implement the fix and develop tests.

[Copilot]

🟢 Approval recommended

The shared-infrastructure refresh changes have no active review issues.

No open issues 🎉

What changed in this PR

Fixes Specify CLI’s integration switch --refresh-shared-infra handling for installed targets, including the current default, using the existing shared installer.

Changes:

• Honors explicit shared refresh while preserving separate teardown consent and the current-default no-flag no-op.
• Expands regression coverage for flag combinations, stored runtimes, manifest integrity, failure handling, and file protections.
• Documents refresh behavior for new, installed, and current-default targets.

File	Description
tests/​specify_cli/​integrations/​test_command_switch.py	Expands refresh regression tests and preservation checks.
src/​specify_cli/​integrations/​command_switch.py	Honors the refresh flag for installed targets and updates CLI help.
docs/​integrations/​cli.md	Clarifies overwrite consent and current-default behavior.

_{Review effort: Balanced (auto)}