[REF] Create custom paths for user guide and data model pages, refactor section on local_nb_nodes.json

[alyssadai]

• Closes Refactor docs such that the Neurobagel user guide is in a dedicated directory #99
• Closes Rename section local_nb_nodes.json to something more informative #241
• Closes Add pattern to markdown link checker config to ignore SNOMED URLs #114

Changes proposed in this pull request:

• Create dedicated subdirectories (paths) for User Guide pages and Data Model pages:
  • neurobagel.org/user_guide/...
  • neurobagel.org/data_models/...
• Turn overview.md into a section index page for the User Guide section (so now, you can navigate to https://neurobagel.org/user_guide directly)
  • For reviewer: we could also do this for the variables.md page under Data Model subdirectory, since that page also kind of acts as an overview page
• Rename section called "local_nb_nodes.json" in the "Configuring a node" page to something more informative, and restructure section for readability

Checklist

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Summary by Sourcery

Refactor documentation structure by creating custom paths for User Guide and Data Model pages, and improve the section on 'local_nb_nodes.json' for clarity.

Enhancements:

• Refactor the section on 'local_nb_nodes.json' to improve readability and provide more informative content.

Documentation:

• Create dedicated subdirectories for User Guide and Data Model pages to improve navigation and organization.
• Turn 'overview.md' into a section index page for the User Guide, allowing direct navigation to the User Guide section.
• Rename and restructure the section on 'local_nb_nodes.json' in the 'Configuring a node' page for better clarity and readability.

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[sourcery-ai]

Reviewer's Guide by Sourcery

This PR reorganizes the documentation structure by creating dedicated subdirectories for User Guide and Data Model pages, and improves the readability of the node configuration documentation. The changes primarily involve moving files into new directories and updating internal documentation links to reflect the new structure.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Reorganized documentation structure with dedicated subdirectories	Created user_guide/ directory for user guide related pages Created data_models/ directory for data model related pages Updated navigation structure in mkdocs.yml to reflect new directory structure Fixed all internal documentation links to match new file paths	mkdocs.yml docs/user_guide/* docs/data_models/*
Improved node configuration documentation	Renamed section from 'local_nb_nodes.json' to 'Configuring node names and URLs for federation' Restructured content for better readability Added JSON example formatting Moved warning about federation API address to a more prominent position	docs/user_guide/config.md
Fixed image paths in documentation	Updated relative paths to images to account for new directory structure	docs/user_guide/annotation_tool.md docs/user_guide/getting_started.md

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#99	Create a dedicated directory for the Neurobagel user guide documentation	✅
#99	Make user guide directly accessible at neurobagel.org/user-guide	✅
#241	Rename the 'local_nb_nodes.json' section in the documentation to be more informative about node naming	✅

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[sourcery-ai]

Hey @alyssadai - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[surchs]

Thanks @alyssadai, this looks great

🧑‍🍳