fix(skills): preserve project and global root scopes

[luoye520ww]

Summary

• Preserve the project/global scope assigned by the GUI skill root discovery service.
• Keep manually configured project and global roots in their matching Kun capability fields.

Root cause

guiSkillRootsForRuntime already labels each root as project or global, but syncGuiManagedKunConfig discarded that label and appended every GUI root to capabilities.skills.roots. The runtime consequently diagnosed and prioritized global skills as project skills.

Changes

• Split GUI-managed roots into roots and globalRoots by their existing scope.
• Filter stale GUI-managed entries from both persisted root lists before rebuilding them.
• Enable the capability when either scoped root list is populated.
• Extend the existing config sync test to assert both fields.

Tests

• npm.cmd test -- src/main/kun-process.test.ts (38 tests)
• npm.cmd run typecheck
• git diff --check

[XingYu-Zhong]

Reviewed and approved for merge.