docs: update v2 config deploy guide for Ubuntu 22.04, JDK 11, Tomcat …

[Hitanshi7556]

Closes #118

This PR updates the Configuration and Deployment Guide for v2.x, which was severely outdated. A previous contributor (gorgwu) attempted this in PR #125 but their fork was deleted This PR picks up that work and discussions

Changes Made

OS and Software Versions

• Debian 9 → Ubuntu 22.04 LTS: Debian 9 is end of life with no security updates. Ubuntu 22.04 is what the official Docker image uses and receives security updates until 2027.
• JDK 8 → JDK 11: OBA now requires JDK 11 as a minimum. Updated install command to openjdk-11-jdk.
• Tomcat 8 → Tomcat 9: Tomcat 8 is not available in Ubuntu 22.04 repos. Tomcat 9 is available via apt-get and all paths updated accordingly (/var/lib/tomcat9/, service tomcat9, etc).
• MySQL Connector/J 5.1.46 → 8.3.0: Updated to match MySQL 8. Filename format also changed from mysql-connector-java-5.1.46-bin.jar to mysql-connector-j-8.3.0.jar.

MySQL Installation

• Ubuntu 22.04 has MySQL 8.0 directly in its repos — the old manual apt-config .deb method is no longer needed.
• MySQL 8 no longer auto-prompts for a root password during install. Added manual root password setup commands using ALTER USER.

Download URLs

• Replaced all hardcoded 2.0.0 version URLs pointing to the dead nexus server with current version 2.5.12-cs from the Cambridge Systematics repo.
• Added a note instructing users to check the Downloads page and substitute the latest version number if a newer one is available.
• Note: Dynamic version substitution via site_metadata.yml is not possible in .md files (only .erb), so the version is kept as a static string with clear instructions.

data-sources.xml Updates

• Updated MySQL driver class from the deprecated com.mysql.jdbc.Driver to com.mysql.cj.jdbc.Driver in all three webapp configs (federation, API, enterprise). This is required for MySQL 8 compatibility.
• Placeholder passwords clearly marked for replacement.
• GTFS realtime configuration preserved.
• Duplicate PropertyOverrideConfigurer bean removed from API webapp config.

Text Fixes

• Removed the blue "out of date" <div> at the top (as requested by @aaronbrethorst in PR Update the "Configuration and Deployment Guide for v2.x" Document #125 — it was added to flag the guide as outdated, and these changes fix that).
• Added a Docker recommendation note at the top directing new users to the official Docker deployment guide.
• Fixed "second-to-last" (was "second-last") in API webapp section.
• Various minor grammar and clarity improvements.

What Was Not Changed

• The data-sources.xml structure was kept largely intact. @aaronbrethorst suggested inspecting a live Docker container to get the latest versions — this is flagged as a follow-up.
• Live server testing on Ubuntu 22.04 + Tomcat 9 was not performed (no server available). Commands are based on known Ubuntu 22.04 package availability and MySQL 8 behavior.

PTAL @aaronbrethorst
I would make the changes sugegsted by you!
thank you

[Copilot]

Pull request overview

Updates the v2.x Configuration and Deployment Guide to reflect a modern/manual install path aligned with the current ecosystem (Ubuntu 22.04, Java 11, Tomcat 9, MySQL 8, updated artifact locations), while encouraging Docker as the preferred deployment approach.

Changes:

• Refreshes the manual install guide for Ubuntu 22.04 + OpenJDK 11 + Tomcat 9 + MySQL 8.
• Updates binary download URLs/version references and the MySQL Connector/J version.
• Updates example data-sources.xml snippets for MySQL 8 (com.mysql.cj.jdbc.Driver) and removes a duplicate Spring bean in the API webapp snippet.

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