Module scope version diagnostics and dependency mismatch handling

[djm81]

Why

A key user reported conflicts and version mismatches when SpecFact modules exist in both project-local scope and user scope across split repos and monorepos. Current discovery gives project scope precedence, but stale user copies and implicit modules-repo source bootstrapping can make the effective runtime hard to diagnose.

What changes

• Add user-facing diagnostics for duplicate module ids across project, user, marketplace, custom, and dev source roots.
• Surface effective vs shadowed module versions and recovery commands.
• Enforce versioned module dependency requirements during install/registration where manifest metadata declares them.
• Preserve project-over-user precedence while making mismatches visible and actionable.

Parent Feature

• [Feature] Marketplace Module Distribution #353 Marketplace Module Distribution
• Parent Epic: [Epic] Architecture (CLI structure, modularity, performance) #194 Architecture (CLI structure, modularity, performance)

Source Tracking

• OpenSpec change: module-scope-version-diagnostics
• Branch: feature/module-scope-version-diagnostics
• Repository: nold-ai/specfact-cli

OpenSpec Change Proposal: module-scope-version-diagnostics