Bug: Review bootstrap must preserve user-scoped modules #452

Problem

Repository bootstrap guidance currently tells agents to uninstall a shadowed user-scoped module when a project-local bundle is present. During specfact code review work this repeatedly removes user-scoped specfact-codebase and specfact-code-review, even though project-over-user shadowing is normal and the user copy is still needed in other repositories.

Expected behavior

• Project-local module sources remain authoritative inside this repository.
• User-scoped modules remain installed and usable outside this repository.
• Bootstrap and repository guidance never prescribe user-scope uninstall as routine shadow cleanup.
• The paired core diagnostics explain shadowing without destructive recovery advice.

Scope

Correct the development bootstrap and repository guidance, and add regression coverage that prevents the destructive instruction from returning. Paired core bug: nold-ai/specfact-cli#699.

Governance

• Parent: specfact code / AI-bloat defense #162
• Blocked by: none
• Blocks: coordinated patch release after both paired pull requests merge
• OpenSpec: module-scope-02-preserve-user-installs

Acceptance criteria

• Tests prove bootstrap/repository guidance does not recommend module uninstall --scope user.
• Guidance states that project scope shadows, but does not delete, the user installation.
• Existing local-bundle import isolation remains unchanged.
• Focused and repository quality gates pass.