Fix environment skill discovery after merge

[jif-oai]

Why

The merge of #29831 with the new fs/walk environment discovery path left three SkillFileDiscovery initializers without the new namespace fields. This makes codex-core-skills fail to compile and breaks CI for every PR based on current main.

What changed

• collect plugin roots from the directory entries already returned by fs/walk
• keep the selected root as the namespace fallback
• initialize empty discovery results with empty namespace sets

This preserves the bounded fs/walk implementation while restoring the namespace caching added by #29831.