Fixes #10 Migrate quali workflow Matlab=>R

[Yuri05]

• Adjusted qualification_plan.json to the latest qualification schema version

  • Switched from old section id to the new section reference
  • Use arrays of observed data sets where possible
  • Remove chapter number from chapter titles
  • Removed "EndTime": "Inf" entries

• Upgraded used models to the latest versions

• Upgraded used observed data to the latest version

• Upgraded used text modules to the latest version

• Report for review: https://github.com/Yuri05/OSP-Qualification-Reports/blob/01_TestMigration_DDI_CYP1A2/DDI_Qualification_CYP1A2/report.md

• PR for comparison with the previous report: Test migration Matlab=>R: DDI_CYP1A2 OSP-Qualification-Reports#62

[Copilot]

Pull Request Overview

This PR migrates the qualification workflow from Matlab to R and updates inputs to match the new qualification schema. Key changes include:

• Implementation of a new R-based workflow script (Qualification/workflow.R) replacing the Matlab version.
• Updates to qualification_plan.json to use the new v3.3 schema including new keys and model release URLs.
• Removal of legacy GitHub workflow files and addition of updated workflows for input file validation, markdown link checking, and model release verification.

Reviewed Changes

Copilot reviewed 11 out of 12 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
Qualification/workflow.R	New R script implementation for running the qualification workflow.
Qualification/Workflow.m	Removal of the legacy Matlab workflow script.
Qualification/Input/qualification_plan.json	Updated schema version, new project/model release URLs, and key renames.
Qualification/Input/Content/Qualification_DDI_network_description.md	Updated model release version numbers in the content.
.github/workflows/XRefCheck.yml	Removal of outdated workflow.
.github/workflows/SpellChecker.yml	Removal of outdated workflow.
.github/workflows/MarkdownLinksCheck.yml	Removal of outdated workflow.
.github/workflows/Check_Links_In_Report.yml	New workflow to check report links and cross-references.
.github/workflows/Check_Input_Files.yml	New workflow for checking input file validity.
.github/workflows/CheckUsingLatestRelease.yml	New workflow to check for the latest model releases.
.github/workflows/CheckForLatestModelReleasesInQualificationPlan.yml	New workflow script to verify that projects are at their latest releases.

[Yuri05]

@PavelBal
Check Latest Model Releases in a Qualification Plan check fails because Fluvoxamine model uses the "alternative version" of the model, which is not the latest release

Qualification-DDI-CYP1A2/Qualification/Input/qualification_plan.json

Lines 12 to 15 in e34e0d9

	{
	"Id": "Fluvoxamine",
	"Path": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Fluvoxamine-Model/alt_v1.0/Fluvoxamine-Model.json"
	},