Documentation: Update vignette to reflect Bioc April 2025 changes

[evaham1]

Update the extended mixOmics vignette to reflect changes and updates in the mixOmics version to be released on Bioconductor April 2025

Includes:

• Updating use of plotting functions to reflect different ways to control colours/pch (plotIndiv(), biplot(), plotArrow())
• Update any sections on tuning and performance assessment to reflect new and edited functions (tune(), perf.assess()), follow what is on the mixOmics webpages
• any other updates and check for general typos in the vignette