Bug: Shadow diagnostics must preserve user-scoped modules

[djm81]

Problem

When a project-scoped module shadows the same user-scoped module, module discovery and specfact module doctor recommend specfact module uninstall <name> --scope user. Review/bootstrap workflows surface that recommendation, and agents can follow it even though shadowing is normal precedence rather than a broken installation. The result is loss of the user-scoped specfact-codebase and specfact-code-review installation for every other repository.

Expected behavior

• Project scope continues to take precedence inside the current repository.
• The shadowed user-scoped module remains installed and usable outside the repository.
• Discovery and doctor diagnostics explain the precedence and state that no action is required.
• No review-triggered or recovery guidance recommends removing the user-scoped copy.
• Explicit user-initiated uninstall behavior remains unchanged.

Scope

Update core module discovery and doctor recovery messaging, with regression tests. Paired modules bug: nold-ai/specfact-cli-modules#452.

Governance

• Parent: [Feature] Marketplace Module Distribution #353
• Blocked by: none
• Blocks: coordinated patch release after both paired pull requests merge
• OpenSpec: module-scope-02-preserve-user-installs

Acceptance criteria

• Tests prove shadow diagnostics contain no user-scope uninstall recommendation.
• Tests prove diagnostics explicitly preserve cross-repository availability.
• Existing project-over-user precedence is unchanged.
• Focused and repository quality gates pass.

[djm81]

Implementation PR: #700. Paired modules PR: nold-ai/specfact-cli-modules#454

[djm81]

Completed by PR #700, merged to dev as 542b461 on 2026-08-30.