[Docs] Directory tree hierarchy discrepancy in README.md

[hot666666]

Description

In the README.md (specifically under Step 2: Create project specifications and Step 4: Generate a plan), the directory tree diagrams show the specs/ directory nested under .specify/:

.specify/
├── memory/
├── scripts/
├── specs/
│   └── 001-my-first-feature/
└── templates/

However, in actual project initialization (for all agents like Claude, Gemini, Codex, etc.), the specs/ directory is created at the project root level, and .specify/ contains memory/, scripts/, and templates/:

.
├── .specify/
│   ├── memory/
│   ├── scripts/
│   └── templates/
└── specs/
    └── 001-my-first-feature/

This issue proposes fixing the directory trees in README.md to accurately represent the actual folder layout.