Organize Scripts into Folders and Refactor Structure

[SeanChangX]

Tasks:

1. Reposition script execution commands to more appropriate locations.
2. Group all scripts into a dedicated folder for better organization.
3. Move miscellaneous files (e.g., .bash, .txt, etc.) from the root directory to a designated folder.
4. Rename env_reset.sh and env_setup.sh with numerical prefixes for better ordering.
5. Test on a clean machine before merging into the dev branch.

Acceptance Criteria:

1. Scripts are properly organized into a structured folder system.
2. Miscellaneous files are no longer in the root directory.
3. env_reset.sh and env_setup.sh follow a clear numerical naming convention.
4. Successfully tested on a fresh environment without issues.