allowManagedPermissionRulesOnly now also withholds allowed-tools from user and project skills

What

When the managed policy setting allowManagedPermissionRulesOnly is on, the allowed-tools list in skill and command frontmatter (the header at the top of a skill file) no longer grants tool permissions unless it comes from a trusted source. Until now the setting covered permission rules from settings files and --allowedTools.

• Ignored: allowed-tools from skills and custom commands in user, project and --add-dir sources, and from plugins adopted from a .claude-plugin manifest inside those skills directories.
• Kept, per the setting's description: other plugins, managed skills and bundled skills. Plugins from the official skills marketplace are exempt.
• Skills and plugin commands now look up their allowed-tools each time they run. When a grant is dropped, a warning is logged, and in text print mode a line on standard error tells you to ask an admin.
• A plugin command whose frontmatter declares PreToolUse or PermissionRequest hooks gets no allowed-tools at all when policy sets disableAllHooks or allowManagedHooksOnly.
• The coordinator no longer tells its workers that a skill grants extra tool permissions when the skill's source or plugin is not trusted under this policy.
• The setting's description now says all of this.

Why

A skill or plugin placed by a user or a repository could previously hand itself tool permissions that the policy meant to keep in the administrator's hands. If you rely on a skill's allowed-tools under this policy, expect permission prompts for those tools, or ask your administrator to add managed rules.