[FEATURE] Per-project plugin configuration and CLI initialization support

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

Currently, Claude Code's plugin system applies globally - plugins enabled in one project remain enabled in all projects. This creates significant workflow friction when working across multiple projects with different requirements:

No project-scoped plugin control: While the documentation mentions repository-level configuration via .claude/settings.json, there is no way to have plugins automatically enable/disable based on the current project directory
No CLI initialization: Unlike other modern dev tools (e.g., npm init, git init), there's no command to initialize project-specific Claude Code configuration
Manual workarounds required: Developers must manually toggle plugins with /plugin enable/disable when switching projects, or maintain their own scripts

Proposed Solution

Add native support for project-scoped plugin management:

Automatic plugin activation: When working in a directory with .claude/settings.json, automatically enable/disable plugins specified in that file
CLI initialization command: Add a command like claude init or claude config init to scaffold basic project configuration:

bash claude init

• Creates .claude/settings.json with interactive prompts
• Optionally initializes CLAUDE.md template

Clear precedence model: Project settings override global settings for plugins, similar to how .gitconfig works

Alternative Solutions

Manual enable/disable: Current workaround, but error-prone and tedious
Shell scripts/aliases: Possible but not portable or standardized
Global-only configuration: Doesn't support multi-project workflows

Priority

Critical - Blocking my work

Feature Category

CLI commands and flags

Use Case Example

This would benefit:

Developers working on multiple projects with different tooling needs (e.g., Python projects needing different plugins than JavaScript projects)
Teams sharing configurations - ensure consistent plugin usage per-project in version control
Consultant/contractor developers switching between client projects frequently
Open source maintainers who work across many repositories

Additional Context

_No response_