feat: minor redesign

[mihai-sysbio]

In this PR, I aimed to refresh/improve the website in preparation for wider usage, by:

• including some calls to action on the landing page
• making the Sources page more user friendly
• streamlining the Documentation page
• simplyfing the navigation bar, including the Publication page

Some further to-dos are suggested below, either as further commits in this PR or to report as separate issues:

• updating the Gitter channel - the current one is for bio.tools
• the mermaid snippet in Documentation fails to be rendered
• the Applications page still used the old/tabular design
• from @supernord's review:
  • placing the governance file in this repo?
  • Copyright statement is missing from the footer
  • Consider adding more links to the footer
  • We can update the tiles on all pages to be more interactive -> as an example here is a link to the tiles used for the Australian structural bio community: https://australian-structural-biology-computing.github.io/activities
  • Title on index page should be Research Software Ecosystem; Another option would be to completely remove this heading, and modify the blue text
    See some screenshots below:

Note: As soon as the other PR gets merged, this one will be only contain the redesign commit.

[supernord]

@mihai-sysbio - I can't modify this PR, so I'll add comments instead to review the changes

[supernord]

Suggested change

	- title: Contributors
	- title: Credits & Contributors

[mihai-sysbio]

I see two issues here:

• navbar items should be short, how about "Contributions"?
• "credits" was just replaced by "Acknowledgements"

[supernord]

@mihai-sysbio / @hmenager

Overall I like the new structure.

Comments below:

• Using v3.0.0 of ETT -> consider moving to 5.0.0
• Copyright statement is missing from the footer
• Consider adding more links to the footer
• We can update the tiles on all pages to be more interactive -> as an example here is a link to the tiles used for the Australian structural bio community: https://australian-structural-biology-computing.github.io/activities
• Title on index page should be Research Software Ecosystem
  • Another option would be to completely remove this heading, and modify the blue text

I suggest the following change to the development process for the website (or something similar to this).

1. Merge the changes here (if others approve)
2. Create a release branch
3. Modify main branch during development
4. When ready, merge main branch with release branch

[mihai-sysbio]

Thank you very much for the review @supernord. Some of the things were easier to address than others.

* Using `v3.0.0` of ETT -> consider moving to `5.0.0`

Done.

* Copyright statement is missing from the footer
* Consider adding more links to the footer
* We can update the tiles on all pages to be more interactive -> as an example here is a link to the tiles used for the Australian structural bio community: https://australian-structural-biology-computing.github.io/activities
* Title on index page should be `Research Software Ecosystem`
  * Another option would be to completely remove this heading, and modify the blue text

All these were added as to-do's in the PR description - I believe that list should be used for a "round 2" of the website redesign. That would allow this PR to be merged while work continues, while keeping PRs smaller and easier to review.

I suggest the following change to the development process for the website (or something similar to this).
1. Merge the changes here (if others approve)
2. Create a release branch
3. Modify main branch during development
4. When ready, merge main branch with release branch

Alternatively, we could aim for smaller and more independent PRs, which would mean that end users get to see changes faster.

[mihai-sysbio]

There were some suggestions for applications.md and contacts.md which only seem to be shuffling content around? It was hard to grasp the desired outcome from the suggestions, it might be easier to talk about these.

[Copilot]

Pull request overview

This PR refreshes and improves the Research Software Ecosystem website in preparation for wider usage through a comprehensive redesign. The changes modernize the user experience with card-based layouts, streamlined navigation, and improved content organization.

Changes:

• Introduced card-based UI components for sources, documentation, and contact pages with improved visual hierarchy
• Restructured navigation by moving Documentation and Contacts to top-level items and consolidating Credits into Contributors page
• Updated ELIXIR toolkit theme from version 3.0.0 to 5.0.0 with corresponding Gemfile.lock updates

Reviewed changes

Copilot reviewed 15 out of 17 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
sources.md	Added card-based layout with registry badges and metadata/workflow links for each source
index.md	Redesigned landing page with call-to-action buttons and three-column feature cards
docs.md	Streamlined documentation with quick-start cards, removed inline citation, improved mermaid diagram formatting
publications.md	Added section headers for Citation and Presentations
contributors.md	Merged Credits page content, renamed to "Credits" with Contributors, Funding, and Acknowledgements sections
credits.md	Converted to redirect page pointing to contributors
contacts.md	Added card-based layout for community support and issue reporting
applications.md	Added introductory text and alert box with guidance
licence.md	Fixed title formatting and line break in license text
_data/topnav.yml	Restructured navigation with Documentation and Contacts as top-level items
_data/tool_and_resource_list.yml	Updated IDs from galaxy_codex to galaxy and debianmed to debian-med
_data/CONTRIBUTORS.yml	Added Mihail Anton as contributor
_config.yml	Updated theme to 5.0.0 and removed duplicate exclude section
Gemfile.lock	Generated lockfile for updated dependencies
404.html	Redesigned error page with Bootstrap styling
_posts/2024-04-29-welcome-to-jekyll.markdown	Removed default Jekyll welcome post

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[hmenager]

Just spotted a minor weirdness with url displays in the source tiles:
. Otherwise, I can't see any reason not to merge this (i.e. not perfect yet, but already improving so much over the previous version!). Thanks a lot for all this work @mihai-sysbio , and to you @supernord for the review!

[mihai-sysbio]

minor weirdness with url displays in the source tiles

Thank you @hmenager for the review and for spotting the weirdness. It has been addressed in 814de63.