feat: use directory structure that supports multiple features

[meylis1998]

Summary

• Restructures specs/ directory to support multiple features with numbered directories (e.g., specs/001-my-app/, specs/002-add-auth/)
• Splits single DESIGN.md into separate files: spec.md, data-model.md, plan.md
• Renames IMPLEMENTATION.md to tasks.md
• Adds checklists/requirements.md for tracking functional/non-functional requirements

New Directory Structure

specs/
  └── NNN-feature-name/
      ├── checklists/
      │   └── requirements.md
      ├── data-model.md
      ├── plan.md
      ├── spec.md
      └── tasks.md

Benefits

• Multiple features: Track multiple features/modifications independently in a single project
• Better organization: Dedicated files for data model, plan, spec, and implementation tasks
• Requirements tracking: Checkbox-based requirement tracking with automatic updates during implementation
• Sequential numbering: Auto-incrementing numbered directories for clear ordering

Closes #47

[gemini-code-assist]

Code Review

This pull request introduces a new, more scalable directory structure for feature specifications, moving from single design files to a numbered directory per feature. This change is consistently applied across the create-app, create-package, and modify commands, improving organization. The changes are well-implemented, but I found one minor factual error in a version number that is repeated across several files. Please see the detailed comment. A helpful fallback instruction for running apps was also added, which is a nice addition.