Plans

Current as of 2026-06-03.

Current State

AgentOS developer-project scaffold has been added: AGENTS.md, prompts/README.md, prompts/architecture.md, and prompts/plans.md.
The site remains a Jekyll/GitHub Pages static website; no site behavior or content was changed by the scaffold.
A durable local Ruby setup has been installed with rbenv under /Users/benbfly/.rbenv; this repo is pinned to Ruby 3.3.4 via .ruby-version, and ~/.zshrc initializes rbenv for fresh zsh shells.
Local rbenv, ruby-build, compiled Ruby, installed gems, and shell initialization affect Ben’s Mac only. GitHub Pages hosting continues to use GitHub’s own Pages runtime.

Maintenance Guidance

Read prompts/architecture.md before changing _config.yml, collections, layouts/includes, data formats, dependencies, build behavior, or deployment behavior.
For content-only edits, update the relevant top-level page or collection Markdown and validate with a Jekyll build when practical.
Keep active prompt files brief; move dated historical detail into prompts/*_deep_records_*.md.

Validation

People page roster update validated on 2026-06-03: Amit Levin, Dolev Revivo, and Yonatan Berg member files were removed; Efrat Katsman was moved to past members; Rohi, Ofri, Efrat, Irene, Devorah, Lior, and Dror titles/current-address/photo metadata were updated; _site/people/index.html rendered the requested names, titles, image, and current-address links, and omitted the removed names. /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing project-layout and Bootstrap deprecation warnings.
People page metadata-field update validated on 2026-06-03: people.md now conditionally renders optional website, orcid, and current_address member front matter. Unambiguous ORCIDs were added for Ben Berman, Efrat Katsman, Shari Orlanski, and Irene Unterman from public article/ORCID evidence; no ORCID was added for other listed members where search results were absent or ambiguous. _site/people/index.html rendered the four expected ORCID links and no empty Website/Current address rows; /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing project-layout and Bootstrap deprecation warnings.
People page content update validated on 2026-06-03: _members/current/030_rohi.md and _members/current/040_ofri.md were added, Efrat/Shari photo front matter was updated to their new images, _site/people/index.html contained the expected names and image paths, and /Users/benbfly/.rbenv/bin/rbenv exec bundle exec jekyll build completed successfully with only the existing project-layout and Bootstrap deprecation warnings.
bundle exec jekyll build was attempted on 2026-06-03. It did not reach a Jekyll build because the local Bundler environment is missing http_parser.rb, required through github-pages -> jekyll-seo-tag -> jekyll -> em-websocket.
Local preview diagnosis on 2026-06-03: Apple system Ruby 2.6.10 and Bundler 1.17.2 are active. The global gems under /Library/Ruby/Gems/2.6.0 have broken/stale native extensions for commonmarker, eventmachine, http_parser.rb, and racc; ffi is also installed as an incompatible x86_64 native gem. A disposable temp bundle succeeded with the project Gemfile plus gem "ffi", "< 1.17.3", then BUNDLE_GEMFILE=/private/tmp/methylgrammarlab-jekyll-preview-test/Gemfile bundle exec jekyll build --source /Users/benbfly/Documents/benbfly.github.io --destination /private/tmp/methylgrammarlab-jekyll-preview-build.
Jekyll preview was verified on 2026-06-03 with BUNDLE_GEMFILE=/private/tmp/methylgrammarlab-jekyll-preview-test/Gemfile bundle exec jekyll serve --source /Users/benbfly/Documents/benbfly.github.io --destination /private/tmp/methylgrammarlab-jekyll-preview-serve --host 127.0.0.1 --port 4000; localhost returned HTTP 200 and the in-app browser loaded http://127.0.0.1:4000/.
Public DNS diagnosis on 2026-06-03: methylgrammarlab.org uses Hover nameservers and resolves to the four GitHub Pages apex A records; www.methylgrammarlab.org is a CNAME to benbfly.github.io; HTTP and HTTPS both return 200 from GitHub Pages. benbermanlab.com uses Hover nameservers but has no apex A record and no www CNAME, so HTTP/HTTPS resolution fails. A forced Host-header test against a GitHub Pages IP for benbermanlab.com returned GitHub 404, consistent with this repo’s single-domain CNAME (methylgrammarlab.org). To use benbermanlab.com as a secondary entry point, configure it as a redirect domain rather than a second direct GitHub Pages alias.
Existing non-blocking build warnings: _projects/015_PMDs.md and _projects/022_ctdna.md request missing layout project; Bootstrap emits a deprecated text-hide() mixin warning.
Durable preview setup completed on 2026-06-03: rbenv and ruby-build were installed under /Users/benbfly/.rbenv; Ruby 3.3.4 was compiled with local OpenSSL and libyaml; .ruby-version was added; ~/.zshrc initializes rbenv; bundle install resolved github-pages 232 and Jekyll 3.10.0; a fresh interactive shell successfully ran bundle exec jekyll build.
Current verified server command: bundle exec jekyll serve --host 127.0.0.1 --port 4000 from a fresh shell in the repo; HTTP response reported WEBrick with Ruby 3.3.4.

Local Jekyll Preview

Open a fresh zsh shell, cd /Users/benbfly/Documents/benbfly.github.io, then run bundle exec jekyll serve.
The current preview server was verified at http://127.0.0.1:4000 using WEBrick with Ruby 3.3.4.
Gemfile.lock is still ignored by .gitignore; do not treat the local lockfile as a source-controlled artifact unless Ben explicitly changes that convention.
If bundle unexpectedly uses /usr/bin/ruby, open a fresh shell or confirm ~/.zshrc still contains the rbenv PATH/init lines.

Safe Resume

Start with git status --short.
Use a fresh shell so rbenv initialization in ~/.zshrc is active.
If preview is already running on port 4000, stop the existing Jekyll process or choose another port.
Do not revert unrelated worktree changes such as .DS_Store or newly added content assets unless Ben explicitly asks.