[WIP] Create manatom folder with README file for atom manipulation tools

[Copilot]

• Create manatom folder in repository root
• Add README.md file to manatom folder with specified content
• Verify the changes

Original prompt

Create a new folder called manatom in the repository root. This folder will contain a tool to manipulate atom positions.

Add a README.md file in the manatom folder with the following content:

# manatom

This directory contains tools for manipulating atom positions.

This pull request was created from Copilot chat.

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