Documentation Update

[frankambrosio3]

🗑️ This dev branch should be deleted after merging to main.

🧠 Summary

This PR updates several aspects of the Theiagen documentation.
It updates the TheiaEuk workflow diagram, fixes several broken links, and adds a more thorough explanation of the tools that are deployed upon detection of Candida auris.
It fixes broken links to workflow task files in documentation pages for TheiaEuk, TheiaProk, TheiaMeta, Augur, Snippy_Tree and NCBI_Scrub.
It adds more thorough explanations of the components of Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree and Snippy_Variants.
It also reformats and adds to the contribution guide.

⚡ Impacted Workflows/Tasks

This PR only modifies documentation. No changes are made to functional code.

This PR may lead to different results in pre-existing outputs: No

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

It updates the TheiaEuk workflow diagram, fixes several broken links, and adds a more thorough explanation of the tools that are deployed upon detection of Candida auris.
It fixes broken links to workflow task files in documentation pages for TheiaEuk, TheiaProk, TheiaMeta, Augur, Snippy_Tree and NCBI_Scrub.
It adds more thorough explanations of the components of Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree and Snippy_Variants.
It also reformats and adds to the contribution guide.

⚙️ Algorithm

This PR only modifies documentation. No changes are made to functional code.

➡️ Inputs

This PR only modifies documentation. No changes are made to functional code.

⬅️ Outputs

This PR only modifies documentation. No changes are made to functional code.

🧪 Testing

I clicked all the links in the docs pages to make sure they are not dead links, and I reviewed the docs from the perspective of a new user.

Suggested Scenarios for Reviewer to Test

This PR only modifies documentation. No changes are made to functional code.

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• [NA] The CI/CD has been adjusted and tests are passing (Theiagen developers)
• [NA] Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)

🎯 Reviewer Checklist

• [NA] All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• [NA] All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated

[sage-wright]

🌟