* Initial structural work to use SCSS for CSS compilation, with new Bootstrap 5.3

* Silence depreciation warnings in the CSS compilation so as not to pollute pre-commit

See twbs/bootstrap#40962 - can hopefully remove these again in a future version of Bootstrap

* Initial structural work for bootstrap5 JS - use Vite for build

* First stab at converting BS3 -> BS5 for HTML in default template

* Document config.development

* Updates for other templates that use default as a base

* Update CLI docs for --development now that vite minimises

* Fix: Make callAfterDecompressed, notEmptyObj, and mqc_plots globally accessible

The JavaScript bundler (Vite) encapsulates variables in module scope, making them inaccessible to external scripts like module-specific JavaScript files (e.g., multiqc_fastqc.js). This caused 'callAfterDecompressed is not defined' errors.

Fixed by explicitly assigning these variables to the window object:
- window.callAfterDecompressed (used by module JS files to register callbacks)
- window.notEmptyObj (utility function used across modules)
- window.mqc_plots (global plot data accessed by multiple files)

This ensures backward compatibility with module JavaScript files that expect these as global variables.

* Make common JS functions global scope

* Add file for bootstrap variables. Overwrite table background colour.

* Get the toolbox to show properly, use md icons instead of emoji

* Start converting hardcoded hex values in custom.css to BS CSS variables

* Minor cleanup

* Smaller base font size. Outline buttons instead of secondary.

* Update how SVG icons are handled, remove all traces of glyphicons

* Fix scoping errors in JS for AI summaries

* Fix buttons that launch modal windows

* New icon for violin plots

* Improve pre-commit build step

* Fix old BS3 form-inline forms

* Start work on toolbox: use offcanvas and BS list group

* Refactor: Split toolbox javascript into multiple files

* Prettier: also format jinja template files

* Prettier formatting

* Fix prettier error

* Initial effort: dark mode toggle

* Replace toast JS library with native Bootstrap toasts

* Nav: make version a link, go to top of page

* Fix 'scroll to top' button

* Start work on fixing the toolbox

* Working on fixing up the sidebar

* Fix toolbox on mobile

* Seqera SVG logos that work in dark mode

* Fix up the footer styling and CSS

* Start small-scale tweaking: buttons

* Make plotly plots respond to theme toggle

* Light-mode plotly python config for exports

* Transparent backgrounds for HTML by default, white only for export

* Work on custom themes by having 2 bootswatch examples

* simplify vite now that the old toast library is gone

* custom.scss - tidy up without changes

* Directly use bootstrap SCSS vars, not var()

* Custom CSS - remove nearly all hardcoded colour and replace with BS variables

* Switch hardcoded border attributes

* Back to css variables to handle dark mode switch

* Don't hardcode fonts

* Start cleaning custom css. Restyle toolbox: about

* No hardcoded breakpoints. More cruft removal

* Clean up some prefixes, some css

* Nicer toolbox buttons in mobile nav

* Update / fix the icon for the side nav toggle button

* More cruft cleaning in custom.scss

* Tidy up footer CSS

* Cleanss

* More tweaking till my brain melts

* Finally figure out how to make child theming work properly

* Bunch of work on getting themes to work properly, improvements to plotly dark mode and more

* Nicer tooltips in dark mode

* Violin plot axes coloured properly on first render

* Dark mode improvements for the violin plot

* Violin plot tooltips - dark mode

* Fix toolbar, allow overflow scroll. Tidy assets.

* Headings top-margin

* Load Seqera AI icon from single file, prefix localstorage dark mode toggle with mqc

* Start working through the toolbox HTML and CSS

* Break toolbox into separate template files

* Update toolbox: hide samples

* Fix AI toolbox errors introduced in AI refactoring, improve layout

* Move AI logos into asset files. Make them work in dark mode.

* Clean up a lot of the AI summary styling

* Update bootstrap tooltips, more AI summaries clean up

* Fix / improve regex help modal. Clean up a load of old CSS

* Fix / update export toolbox pane

* Fix / update export toolbox pane

* Update the citations toolbox tab

* Final tidying on custom.scss

* Start working on the fastqc status bars

* Fix FastQC progress, popover and tooling. And DOIs and some other stuff.

* Make FastQC statuses a generic MultiQC feature

* Table scatter plots: fix for dark mode

* Remove unused javascript variables

* Small refactor theme watcher. Remove update plots call on first load

* Fix bug for dark mode on page load

* Fix plot export button functionality

* Remove last reminants of glyphicons

* Rename theme 'crazy' to 'disco'

* Add back the old template, called 'original'

* Proper spacing in welcome header

* switch to custom plotly bundle in bootstrap-upgrade branch (#3365)

* Don't import unused bootstrap SCSS

* Add description of plotly custom bundle build

* Remove typo $ symbol

* Several small dark mode fixes

* Mixture of module-specific colour fixes for dark mode

* Fix expand / collapse table button

* Disco: remove SCSS imports for unused bootstrap components

* AI summaries: format highlighted text even when not a sample ID

* AI summary highlight colours that work in both themes

* Fix 'scroll to top' button

* Disco SCSS formatting

* Add some custom CSS to 'original' to try to cater for Bootstrap 5 class names in main MultiQC

* Revert changes in templates that inherit from 'original'

* Add a .gitattributes to mark generated files

* Run pre-commit / prettier on all files

* Try to fix CI tests

* Add prettier itself to the hook dependencies

* Pin prettier dep version

* Try fixing CI error with pre-commit jinja plugin

See https://stackoverflow.com/questions/78708497/prettier-plugins-not-found-with-pre-commit

* Docs tweaks

* Ok fine maybe that does need single quotes after all?

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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>