Summary

What You Just Cloned

• This is the AcademicPages Jekyll theme (Minimal Mistakes derivative) wired for GitHub Pages, so you get turnkey layouts for an academic CV site plus helper scripts for publications, talks, and maps.
• All site-wide knobs live in _config.yml, while navigation labels and any future multilingual/UI tweaks live in _data/.
• GitHub Pages will build automatically from main, but you can preview locally with bundle install && jekyll serve -l -H localhost. Docker (docker compose up) is pre-configured if you would rather not install Ruby.

Site-Wide Configuration

• _config.yml holds the title, base URL, sidebar bio, social links, default layouts, enabled collections, and global theme (site_theme: default vs air). Update this first so metadata, feeds, and SEO tags are correct.
• _data/navigation.yml defines the order and URLs of the header menu. Add/remove entries to surface or hide sections (e.g., new pages, CV flavor, external links).
• _data/ui-text.yml lets you rename built-in UI strings (e.g., “Posts”, “Read More”) if you want different phrasing.

Content Buckets You Can Customize

• Blog posts (_posts/): Markdown files must follow the YYYY-MM-DD-title.md convention with front matter for title, tags, and optional permalink. Draft new ideas in _drafts/ until you are ready to publish.
• Standalone pages (_pages/): Anything from About, CV, Publications, custom landing pages, etc. Give each file front matter with permalink and title, then link it through navigation.yml or inline buttons.
• Portfolio items (_portfolio/): Front matter controls teaser text or inline images (see excerpt HTML). Markdown or HTML both work, so you can embed figures, slides, or video.
• Publications (_publications/): Each file stores venue metadata plus optional paperurl, slidesurl, and bibtexurl. These surface automatically wherever publications are rendered, so you just need to drop PDFs/slides in files/ and update the URLs.
• Talks (_talks/) and Teaching (_teaching/): Similar front matter-driven pages for seminars/lectures or course entries. You can add slidesurl, video, or location fields to show action buttons and badges.
• Supporting data: files/ exposes uploads at https://<username>.github.io/files/... (great for CV PDFs, slides, poster images). images/ and assets/ hold static media referenced in posts or CSS.

Figures, Media, and Slides

• Store figures under images/ (keep logical subfolders such as images/research/experiment1.png). Reference them via standard Markdown (![caption](/images/...)) or HTML if you need sizing classes.
• Hero images/backgrounds can also be attached via header: front matter on any page/post.
• Upload decks, posters, and datasets to files/ so you can link using relative URLs; GitHub Pages will serve them verbatim. Use slidesurl, paperurl, posterurl, etc., in front matter wherever you need download buttons.
• Custom fonts/colors: tweak _sass/ and assets/css/main.scss (or switch site_theme) for branding; for quick palette changes, override variables in a new partial and import it into main.scss.

Automation Helpers

• markdown_generator/ contains TSV -> Markdown scripts/notebooks for bulk-importing publications or talks. Update the TSVs with your citation data, run the notebook/script, and copy the generated Markdown into _publications/ or _talks/.
• talkmap/ + talkmap.py can build a leaflet map of your speaking history based on _talks/ metadata (enable talkmap_link in _config.yml once you have real data).

Recommended Adaptation Path

1. Update _config.yml with your name, bio, site URL, theme choice, and analytics IDs. Double-check social links and contact info.
2. Rewrite the key _pages/ content (about.md, cv.md, publications.html, etc.) so each page reflects your research story; hide anything you do not need by removing it from navigation.yml.
3. Migrate your blog posts into _posts/ (or _drafts/ while editing). Use tags and categories to power the archive pages already wired into the theme.
4. Drop figures into images/ and slides/posters into files/, then reference them via front matter or inline Markdown wherever relevant (portfolio cards, publication entries, talk pages).
5. Add portfolio case studies under _portfolio/ to highlight projects beyond papers (embed figures/gifs directly in the Markdown to keep things visual).
6. Use the publication/talk generators if you have structured data; otherwise, hand-author Markdown files with the provided examples as templates.
7. Preview locally, iterate on styling (SCSS, theme setting), then push to the main branch of <username>.github.io to go live.

This repo already mirrors most components you need (blog, CV, publications, course list, talks, portfolio). Treat each folder as a content type, keep media in images/ or files/, and control presentation through front matter plus _config.yml.