Copy over the plugins

.gitignore

@@ -9,3 +9,4 @@ vendor/
 
 # macOS
 .DS_Store
+/_includes/notes_graph.json

_notes/test.md

@@ -4,3 +4,5 @@ layout: default
 ---
 
 Hello World
+
+==This is some highlighted text==

_plugins/bidirectional_links_generator.rb

@@ -0,0 +1,111 @@
+# frozen_string_literal: true
+class BidirectionalLinksGenerator < Jekyll::Generator
+  def generate(site)
+    graph_nodes = []
+    graph_edges = []
+
+    all_notes = site.collections['notes'].docs
+    all_pages = site.pages
+
+    all_docs = all_notes + all_pages
+
+    link_extension = !!site.config["use_html_extension"] ? '.html' : ''
+
+    # Convert all Wiki/Roam-style double-bracket link syntax to plain HTML
+    # anchor tag elements (<a>) with "internal-link" CSS class
+    all_docs.each do |current_note|
+      all_docs.each do |note_potentially_linked_to|
+        note_title_regexp_pattern = Regexp.escape(
+          File.basename(
+            note_potentially_linked_to.basename,
+            File.extname(note_potentially_linked_to.basename)
+          )
+        ).gsub('\_', '[ _]').gsub('\-', '[ -]').capitalize
+
+        title_from_data = note_potentially_linked_to.data['title']
+        if title_from_data
+          title_from_data = Regexp.escape(title_from_data)
+        end
+
+        new_href = "#{site.baseurl}#{note_potentially_linked_to.url}#{link_extension}"
+        anchor_tag = "<a class='internal-link' href='#{new_href}'>\\1</a>"
+
+        # Replace double-bracketed links with label using note title
+        # [[A note about cats|this is a link to the note about cats]]
+        current_note.content.gsub!(
+          /\[\[#{note_title_regexp_pattern}\|(.+?)(?=\])\]\]/i,
+          anchor_tag
+        )
+
+        # Replace double-bracketed links with label using note filename
+        # [[cats|this is a link to the note about cats]]
+        current_note.content.gsub!(
+          /\[\[#{title_from_data}\|(.+?)(?=\])\]\]/i,
+          anchor_tag
+        )
+
+        # Replace double-bracketed links using note title
+        # [[a note about cats]]
+        current_note.content.gsub!(
+          /\[\[(#{title_from_data})\]\]/i,
+          anchor_tag
+        )
+
+        # Replace double-bracketed links using note filename
+        # [[cats]]
+        current_note.content.gsub!(
+          /\[\[(#{note_title_regexp_pattern})\]\]/i,
+          anchor_tag
+        )
+      end
+
+      # At this point, all remaining double-bracket-wrapped words are
+      # pointing to non-existing pages, so let's turn them into disabled
+      # links by greying them out and changing the cursor
+      current_note.content = current_note.content.gsub(
+        /\[\[([^\]]+)\]\]/i, # match on the remaining double-bracket links
+        <<~HTML.delete("\n") # replace with this HTML (\\1 is what was inside the brackets)
+          <span title='There is no note that matches this link.' class='invalid-link'>
+            <span class='invalid-link-brackets'>[[</span>
+            \\1
+            <span class='invalid-link-brackets'>]]</span></span>
+        HTML
+      )
+    end
+
+    # Identify note backlinks and add them to each note
+    all_notes.each do |current_note|
+      # Nodes: Jekyll
+      notes_linking_to_current_note = all_notes.filter do |e|
+        e.url != current_note.url && e.content.include?(current_note.url)
+      end
+
+      # Nodes: Graph
+      graph_nodes << {
+        id: note_id_from_note(current_note),
+        path: "#{site.baseurl}#{current_note.url}#{link_extension}",
+        label: current_note.data['title'],
+      } unless current_note.path.include?('_notes/index.html')
+
+      # Edges: Jekyll
+      current_note.data['backlinks'] = notes_linking_to_current_note
+
+      # Edges: Graph
+      notes_linking_to_current_note.each do |n|
+        graph_edges << {
+          source: note_id_from_note(n),
+          target: note_id_from_note(current_note),
+        }
+      end
+    end
+
+    File.write('_includes/notes_graph.json', JSON.dump({
+      edges: graph_edges,
+      nodes: graph_nodes,
+    }))
+  end
+
+  def note_id_from_note(note)
+    note.data['title'].bytes.join
+  end
+end

_plugins/empty_front_matter_note_injector.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+EMPTY_FRONT_MATTER = <<~JEKYLL
+  ---
+  ---
+
+JEKYLL
+
+# Inject empty front matter in notes that don't have any
+Jekyll::Hooks.register :site, :after_init do |site|
+  Dir.glob(site.collections['notes'].relative_directory + '/**/*.md').each do |filename|
+    raw_note_content = File.read(filename)
+    unless raw_note_content.start_with?('---')
+      raw_note_content.prepend(EMPTY_FRONT_MATTER)
+      File.write(filename, raw_note_content)
+    end
+  end
+end

_plugins/last_modified_at_generator.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+require 'fileutils'
+require 'pathname'
+require 'jekyll-last-modified-at'
+
+module Recents
+  # Generate change information for all markdown pages
+  class Generator < Jekyll::Generator
+    def generate(site)
+      items = site.collections['notes'].docs
+      items.each do |page|
+        timestamp = Jekyll::LastModifiedAt::Determinator.new(site.source, page.path, '%FT%T%:z').to_s
+        page.data['last_modified_at_timestamp'] = timestamp
+      end
+    end
+  end
+end

_plugins/markdown-highlighter.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+# Turns ==something== in Markdown to <mark>something</mark> in output HTML
+
+Jekyll::Hooks.register [:notes], :pre_render do |doc|
+  replace(doc)
+end
+
+Jekyll::Hooks.register [:pages], :pre_render do |doc|
+  # jekyll considers anything at the root as a page,
+  # we only want to consider actual pages
+  next unless doc.path.start_with?('_pages/')
+  replace(doc)
+end
+
+def replace(doc)
+  doc.content.gsub!(/==+([^ ](.*?)?[^ .=])==+/, "<mark>\\1</mark>")
+end

_plugins/open_external_links_in_new_tab.rb

@@ -0,0 +1,28 @@
+# If the configuration sets `open_external_links_in_new_tab` to a truthy value,
+# add 'target=_blank' to anchor tags that don't have `internal-link` class
+
+# frozen_string_literal: true
+require 'nokogiri'
+
+Jekyll::Hooks.register [:notes], :post_convert do |doc|
+  convert_links(doc)
+end
+
+Jekyll::Hooks.register [:pages], :post_convert do |doc|
+  # jekyll considers anything at the root as a page,
+  # we only want to consider actual pages
+  next unless doc.path.start_with?('_pages/')
+  convert_links(doc)
+end
+
+def convert_links(doc)
+  open_external_links_in_new_tab = !!doc.site.config["open_external_links_in_new_tab"]
+
+  if open_external_links_in_new_tab
+    parsed_doc = Nokogiri::HTML::DocumentFragment.parse(doc.content)
+    parsed_doc.css("a:not(.internal-link):not(.footnote):not(.reversefootnote)").each do |link|
+      link.set_attribute('target', '_blank')
+    end
+    doc.content = parsed_doc.inner_html
+  end
+end