Fix mkdocs build issues and clean up documentation

- Fix broken anchor links in perfusionModels.md and perfusionProcesses.md
- Fix case sensitivity issues in nav (AnalysisToolboxes.md, SampleDatasets.md)
- Remove non-existent softwareOverview.md from nav
- Add missing pages to nav (practical-examples, quick-reference, style-guide)
- Rename improved-contribution-tutorial.md to contributionTutorial.md
- Change system preference icon from chainlink to brightness-auto

Author: ltorres6