Remove old setup.sh

[paul-nechifor]

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[greptile-apps]

Greptile Summary

This PR removes an outdated automated setup script (setup.sh) and its associated documentation from the Docker navigation directory. The 706-line shell script provided automated Ubuntu system setup with Docker installation, Git LFS configuration, and repository cloning. This functionality has been superseded by manual Docker build procedures documented in the README. The removal is clean with no external references to the deleted script, and includes removal of a documentation section that contained an embedded GitHub token in a download URL—eliminating a potential security exposure.

Confidence Score: 5/5

• This PR is safe to merge with zero risk—it only removes deprecated code and documentation.
• The PR consists entirely of deletions: removing a deprecated setup script and outdated documentation. No new code is introduced, and the deleted script has no references elsewhere in the codebase. The removal also eliminates a potential security concern (an embedded GitHub token in a download URL). There are no breaking changes since the current documentation provides alternative setup methods.
• No files require special attention

Important Files Changed

Filename	Overview
docker/navigation/README.md	Removed outdated "New Ubuntu Installation" section that referenced the old setup.sh script. The section included an installation URL with an embedded GitHub token, which is also removed. Current documentation remains focused on the manual build and Docker-based approaches, which are the active methods for setup.
docker/navigation/setup.sh	Deleted 706-line shell script that provided automated setup for Ubuntu systems. The script is no longer needed and has been superseded by the manual Docker build and container start procedures documented in README.md. No references to this script exist elsewhere in the codebase.

Sequence Diagram

sequenceDiagram
    participant User
    participant Old Setup Script
    participant README Documentation
    participant Manual Build Process

    User->>Old Setup Script: Runs setup.sh (deprecated)
    Old Setup Script->>Old Setup Script: Installs Docker
    Old Setup Script->>Old Setup Script: Configures SSH keys
    Old Setup Script->>Old Setup Script: Clones repository
    Old Setup Script->>User: Completes setup

    Note over User,Old Setup Script: This flow is removed in PR #888

    User->>README Documentation: Reads manual instructions
    README Documentation->>Manual Build Process: References docker build
    Manual Build Process->>User: Provides current setup method

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