chore: remove SkillMetadata.permissions and derive skill sandboxing from permission_profile (#13061)

## Summary

This change removes the compiled permissions field from skill metadata
and keeps permission_profile as the single source of truth.

Skill loading no longer compiles skill permissions eagerly. Instead, the
zsh-fork skill escalation path compiles `skill.permission_profile` when
it needs to determine the sandbox to apply for a skill script.

  ## Behavior change

  For skills that declare:
```
  permissions: {}
```
we now treat that the same as having no skill permissions override,
instead of creating and using a default readonly sandbox. This change
makes the behavior more intuitive:

  - only non-empty skill permission profiles affect sandboxing
- omitting permissions and writing permissions: {} now mean the same
thing
- skill metadata keeps a single permissions representation instead of
storing derived state too

Overall, this makes skill sandbox behavior easier to understand and more
predictable.

codex-rs/tui/src/bottom_pane/mod.rs

@@ -1539,7 +1539,6 @@ mod tests {
                 dependencies: None,
                 policy: None,
                 permission_profile: None,
-                permissions: None,
                 path_to_skills_md: PathBuf::from("test-skill"),
                 scope: SkillScope::User,
             }]),