[Feature Request] Add flag to ignore user-scoped skills, agents, and MCP configs for deterministic project isolation

Bug Description
User-scoped 'skills' and 'agents' are always enabled. This is not desirable when working with mutiple projects folders that expect a deterministic set of dependencies.

Taking skills for example, it is at the discretion of the skill author if a skill can be automatically invoked based on front matter properties. An inconsiderate skill at User-scope may "leak" into sessions, causing unexpected behavior.

CLI should support a '--project-only' or 'CLAUDE_IGNORE_USER_CONFIG' flag to ensure that no User-scoped skills, agents, hooks, mcps, plugins, commands are made available.

Environment Info

• Platform: darwin
• Terminal: vscode
• Version: 2.1.72
• Feedback ID: fb1b93dd-c123-4e8b-9d57-88773f6a2018