docs: restructure docs and update branding

[svedziok]

This PR reorganizes the MkDocs documentation into a new top-level structure and updates project branding from “ELIXIR Cloud & AAI” / “ELIXIR::GA4GH Cloud” to “ELIXIR-on-Cloud”.

• Reworked MkDocs navigation and site metadata in mkdocs.yml
• Moved documentation pages into a new folder layout matching the new nav:
  • General, Sandbox, Services, Tutorials, Contribute, About
• Updated internal links after the move (landing page buttons + cross-page links)
• Updated project naming across docs/config to “ELIXIR-on-Cloud”
• add index.md files with section summaries

Summary by Sourcery

Restructure the documentation into a new top-level navigation and folder layout while updating all visible branding from “ELIXIR Cloud & AAI” / “ELIXIR::GA4GH Cloud” to “ELIXIR-on-Cloud”.

Documentation:

• Reorganize MkDocs navigation into General, Sandbox, Services, Tutorials, Contribute, and About sections with new index pages and updated landing-page entry points.
• Move and retitle user, admin, and contributor docs into the new structure and adjust internal cross-links accordingly.
• Refresh site metadata, titles, and copy across docs and templates to consistently use the ELIXIR-on-Cloud name and branding.

[sourcery-ai]

Reviewer's Guide

Rebrands the documentation site to “ELIXIR-on-Cloud” and restructures the MkDocs content/navigation into topic-based sections (General, Sandbox, Services, Tutorials, Contribute, About), updating page locations, links, and section landing pages accordingly.

Flow diagram for updated MkDocs navigation structure

flowchart TD
  Home[index]

  Home --> General
  Home --> Sandbox
  Home --> Services
  Home --> Tutorials
  Home --> Contribute
  Home --> About

  General --> GeneralIndex[general/index]
  General --> GA4GHCloudWorkstream[general/ga4gh_cloud]
  General --> SensitiveData[general/sensitive_data]
  General --> UserStories[general/user_stories]

  Sandbox --> SandboxIndex[sandbox/index]

  Services --> ServicesIndex[services/index]
  Services --> CloudRegistry[services/cloudregistry]
  Services --> CWLWES[services/cwlwes]
  Services --> DRSFiler[services/drsfiler]
  Services --> Funnel[services/funnel]
  Services --> LSLogin[services/services_to_ls_aai]
  Services --> proWES[services/prowes]
  Services --> proTES[services/protes]
  Services --> TESK[services/tesk]
  Services --> TRSFiler[services/trsfiler]

  Tutorials --> TutorialsIndex[tutorials/index]
  Tutorials --> SPEBasedOnWES[tutorials/sensitive_data_analysis]
  Tutorials --> Crypt4GHWithProTES[tutorials/crypt4gh_to_protes]

  Contribute --> ContributeIndex[contribute/index]
  Contribute --> Workflow[contribute/workflow]
  Contribute --> GeneralGuidelines[contribute/general-guidelines]
  Contribute --> ManagingProjects[contribute/managing-projects]
  Contribute --> LangSpecific[contribute/language-specific/index]
  LangSpecific --> Python[contribute/language-specific/python]

  About --> Contact[about/contact]
  About --> License[about/license]
  About --> CodeOfConduct[about/code-of-conduct]
  About --> Privacy[about/privacy]
  About --> Imprint[about/imprint]
  About --> Acknowledgements[about/acknowledgements]

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Flow diagram for file moves from guides to new structure

flowchart LR
  subgraph OldGuides
    OGIndex[guides/index]
    OGUserIndex[guides/guide-user/index]
    OGUserStories[guides/guide-user/user_stories]
    OGAdminCWLWES[guides/guide-admin/cwlwes]
    OGAdminSDA[guides/guide-admin/sensitive_data_analysis]
    OGAdminServicesToLSAAI[guides/guide-admin/services_to_ls_aai]
    OGContributorIndex[guides/guide-contributor/index]
    OGContributorWorkflow[guides/guide-contributor/workflow]
    OGContributorGeneral[guides/guide-contributor/general-guidelines]
    OGContributorManaging[guides/guide-contributor/managing-projects]
    OGContributorLangIndex[guides/guide-contributor/language-specific/index]
    OGContributorPython[guides/guide-contributor/language-specific/python]
  end

  subgraph NewStructure
    NGGeneralIndex[general/index]
    NGGA4GHCloud[general/ga4gh_cloud]
    NGUserStories[general/user_stories]
    NGSandboxIndex[sandbox/index]

    NGServicesIndex[services/index]
    NGCWLWES[services/cwlwes]
    NGServicesToLSAAI[services/services_to_ls_aai]

    NGTutorialsIndex[tutorials/index]
    NGSDA[tutorials/sensitive_data_analysis]
    NGCrypt4GH[tutorials/crypt4gh_to_protes]

    NGContributeIndex[contribute/index]
    NGWorkflow[contribute/workflow]
    NGGeneralGuidelines[contribute/general-guidelines]
    NGManagingProjects[contribute/managing-projects]
    NGLangIndex[contribute/language-specific/index]
    NGPython[contribute/language-specific/python]
  end

  OGUserIndex --> NGSandboxIndex
  OGUserIndex --> NGGA4GHCloud
  OGUserStories --> NGUserStories

  OGAdminCWLWES --> NGCWLWES
  OGAdminSDA --> NGSDA
  OGAdminServicesToLSAAI --> NGServicesToLSAAI

  OGContributorIndex --> NGContributeIndex
  OGContributorWorkflow --> NGWorkflow
  OGContributorGeneral --> NGGeneralGuidelines
  OGContributorManaging --> NGManagingProjects
  OGContributorLangIndex --> NGLangIndex
  OGContributorPython --> NGPython

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Flow diagram for branding updates across documentation

flowchart LR
  subgraph OldBranding
    OBName1[ELIXIR_Cloud_and_AAI]
    OBName2[ELIXIR_double_colon_GA4GH_Cloud]
  end

  subgraph NewBranding
    NBName[ELIXIR_on_Cloud]
  end

  OBName1 --> NBName
  OBName2 --> NBName

  subgraph AffectedLocations
    MKDocsYML[mkdocs_yml_site_name_copyright_social]
    Custom404[custom_theme_404_html_titles_labels]
    DocsIndex[docs_index_md_landing]
    ContributeIndex[docs_contribute_index_md]
    CWLWES[docs_services_cwlwes_md]
    ServicesToLSAAI[docs_services_services_to_ls_aai_md]
    CodeOfConduct[docs_about_code_of_conduct_md]
    README[README_md]
  end

  NBName --> MKDocsYML
  NBName --> Custom404
  NBName --> DocsIndex
  NBName --> ContributeIndex
  NBName --> CWLWES
  NBName --> ServicesToLSAAI
  NBName --> CodeOfConduct
  NBName --> README

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File-Level Changes

Change	Details	Files
Reworked MkDocs site configuration to adopt the new information architecture and branding.	Updated copyright, social link labels, and site_name to use the ELIXIR-on-Cloud name. Replaced the old Guides-based navigation with top-level sections: General, Sandbox, Services, Tutorials, Contribute, and About. Pointed navigation entries to the new folder structure and index pages under docs/.	mkdocs.yml
Introduced new section landing pages and reorganized existing content into the new folder layout.	Created new index pages for General, Sandbox, and Tutorials sections with brief overviews and intra-section link lists. Moved user-guide introductory content into a new GA4GH Cloud Workstream page under docs/general/ga4gh_cloud.md. Removed the deprecated guides/landing pages (guide-dev, guides/index) in favor of the new structure.	docs/general/index.md docs/sandbox/index.md docs/tutorials/index.md docs/general/ga4gh_cloud.md docs/guides/guide-dev/index.md docs/guides/index.md
Updated landing page routing and cross-page links to match the new structure.	Changed homepage CTA buttons for Users, Administrators, and Contributors to point to sandbox, services, and contribute index pages respectively. Fixed relative links in contributor docs to point to the new locations of contact, code-of-conduct, images, and LS Login docs. Adjusted internal references from legacy guides paths to the new General/Sandbox/Services/Tutorials/Contribute paths.	docs/index.md docs/contribute/index.md docs/contribute/general-guidelines.md docs/contribute/managing-projects.md docs/contribute/workflow.md docs/general/user_stories.md docs/tutorials/sensitive_data_analysis.md
Renamed and relocated guide content into new topic-based sections (General, Services, Tutorials, Contribute).	Moved user stories from guides/guide-user to docs/general/user_stories.md and updated references. Moved admin service docs (e.g., cwlwes, services_to_ls_aai) under docs/services/ and adjusted in-page project/branding text. Moved contributor guidelines and language-specific Python guide under docs/contribute/ and fixed relative links.	docs/general/user_stories.md docs/services/cwlwes.md docs/services/services_to_ls_aai.md docs/contribute/index.md docs/contribute/general-guidelines.md docs/contribute/managing-projects.md docs/contribute/language-specific/python.md docs/contribute/workflow.md
Applied ELIXIR-on-Cloud branding consistently across documentation and theme templates, and corrected minor typos.	Replaced textual occurrences of “ELIXIR Cloud & AAI” / “ELIXIR::GA4GH Cloud” with “ELIXIR-on-Cloud” in docs, README, and service descriptions. Updated the 404.html custom theme template title, labels, and aria attributes to use the new site name. Fixed several spelling and wording issues (e.g., environments, workflows, excluding, involvement, exciting).	custom_theme/404.html README.md docs/index.md docs/contribute/index.md docs/services/cwlwes.md docs/about/code-of-conduct.md docs/tutorials/sensitive_data_analysis.md docs/contribute/language-specific/python.md docs/general/ga4gh_cloud.md

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[sourcery-ai]

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

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[Copilot]

Pull request overview

This PR reorganizes the MkDocs documentation structure and updates project branding from "ELIXIR Cloud & AAI" / "ELIXIR::GA4GH Cloud" to "ELIXIR-on-Cloud".

Changes:

• Restructured documentation navigation into six top-level sections: General, Sandbox, Services, Tutorials, Contribute, and About
• Updated all branding references from "ELIXIR Cloud & AAI" and "ELIXIR::GA4GH Cloud" to "ELIXIR-on-Cloud"
• Added comprehensive index.md files for each major section with summaries and navigation aids

Reviewed changes

Copilot reviewed 20 out of 36 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
mkdocs.yml	Updated site name, navigation structure, copyright, and social media references to use new branding and folder layout
docs/index.md	Updated landing page with new branding and updated navigation links to reflect new folder structure
docs/tutorials/*	Added new tutorial section with two comprehensive guides on secure genomic analysis (Crypt4GH integration and SPE setup)
docs/services/*	Moved and added service deployment documentation (TESK, Funnel, proTES, proWES, DRS-Filer, TRS-Filer, Cloud-Registry, CWL-WES, LS Login)
docs/general/*	Created new general section with GA4GH Cloud overview, sensitive data processing guidelines, and user stories
docs/contribute/*	Moved contributor documentation with updated internal links
docs/sandbox/index.md	Added placeholder for sandbox/user guide section
custom_theme/404.html	Updated 404 page branding
README.md	Updated project description with new branding

Comments suppressed due to low confidence (8)

docs/contribute/index.md:72

• The word "exiciting" is misspelled and should be "exciting".
  docs/general/ga4gh_cloud.md:113
• The word "environements" is misspelled and should be "environments".
  docs/general/ga4gh_cloud.md:114
• The word "accross" is misspelled and should be "across".
  docs/general/ga4gh_cloud.md:120
• The word "retrievess" should be "retrieves" (extra 's' at the end).
  docs/general/ga4gh_cloud.md:132
• The word "worflows" is misspelled and should be "workflows".
  docs/tutorials/sensitive_data_analysis.md:47
• The word "evironment" is misspelled and should be "environment".
  docs/contribute/language-specific/python.md:9
• The word "exclusing" is misspelled and should be "excluding".
  docs/contribute/index.md:64
• The word "involvment" is misspelled and should be "involvement".

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[uniqueg]

Good stuff!! 🙏 Just a few minor comments

[uniqueg]

LGTM - thanks a lot! 🙏