Feature: Distinguish reused terms in tree view

Gemfile

@@ -1,94 +1,120 @@
 source 'https://rubygems.org'
 
+# Main Rails gem
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
 gem 'rails', '7.0.7'
 
+# JavaScript bundling for Rails
 gem 'jsbundling-rails'
+
+# Chart.js integration for Rails
 gem 'chart-js-rails'
-gem 'sassc-rails' #sass-rails replacent
-gem 'terser' #ugilifer replacent
 
-# See https://github.com/rails/execjs#readme for more supported runtimes
-# gem 'therubyracer', platforms: :ruby
-# gem 'duktape'
+# SassC as a replacement for sass-rails
+gem 'sassc-rails' # sass-rails replacement
+
+# Terser JavaScript minifier as a replacement for Uglifier
+gem 'terser' # uglifier replacement
 
+# Bootstrap front-end framework
 gem 'bootstrap', '~> 4.2.0'
-gem 'jquery-rails'
-gem 'jquery-ui-rails'
 
+# jQuery integration for Rails
+gem 'jquery-rails'
 
+# jQuery UI integration for Rails
+gem 'jquery-ui-rails'
 
-# The original asset pipeline for Rails [https://github.com/rails/sprockets-rails]
+# The original asset pipeline for Rails
+# [https://github.com/rails/sprockets-rails]
 gem 'sprockets-rails'
 
-
-# Use the Puma web server [https://github.com/puma/puma]
+# Use the Puma web server
+# [https://github.com/puma/puma]
 gem 'puma', '~> 5.0'
 
-# Use JavaScript with ESM import maps [https://github.com/rails/importmap-rails]
+# Use JavaScript with ESM import maps
+# [https://github.com/rails/importmap-rails]
 gem 'importmap-rails'
 
-# Hotwire's SPA-like page accelerator [https://turbo.hotwired.dev]
+# Hotwire's SPA-like page accelerator
+# [https://turbo.hotwired.dev]
 gem 'turbo-rails'
 
-# Hotwire's modest JavaScript framework [https://stimulus.hotwired.dev]
+# Hotwire's modest JavaScript framework
+# [https://stimulus.hotwired.dev]
 gem 'stimulus-rails'
 
-# Build JSON APIs with ease [https://github.com/rails/jbuilder]
-#gem "jbuilder"
-
-# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
-gem 'tzinfo-data', platforms: %i[ mingw mswin x64_mingw jruby ]
-
-# To use ActiveModel has_secure_password
-# gem 'bcrypt-ruby', '~> 3.0.0'
+# Time zone info for Windows platforms
+gem 'tzinfo-data', platforms: %i[mingw mswin x64_mingw jruby]
 
 # Reduces boot times through caching; required in config/boot.rb
-
 gem 'bootsnap', require: false
 
-gem 'cube-ruby', require: 'cube'
+# Memcached client for Ruby
 gem 'dalli'
-gem 'flamegraph'
+
+# GraphQL client for Ruby
 gem 'graphql-client'
+
+# Haml template engine for Ruby on Rails
 gem 'haml', '~> 5.1'
+
+# Internationalization (i18n)
 gem 'i18n'
 gem 'rails-i18n', '~> 7.0.0'
-gem 'iconv'
-gem 'multi_json'
+
+# MySQL database adapter
 gem 'mysql2'
+
+# JSON parsing libraries
+gem 'multi_json'
 gem 'oj'
-gem 'open_uri_redirections'
-gem 'pry'
-gem 'psych', '< 4'
-gem 'rack-mini-profiler'
-gem 'rails_autolink'
-gem 'rdoc'
+
+# Google reCAPTCHA integration
 gem 'recaptcha', '~> 5.9.0'
+
+# Simple HTTP and REST client for Ruby
 gem 'rest-client'
-gem 'stackprof', require: false
-gem 'thin'
+
+# View components framework for Rails
+gem 'lookbook', '~> 1.5.5'
 gem 'view_component', '~> 2.72'
-gem 'turnout'
+
+# Pagination library for Rails
 gem 'will_paginate', '~> 3.0'
+
+# Render SVG files in Rails views
 gem 'inline_svg'
-gem "lookbook", '~> 1.5.5'
+
+# ISO language codes and flags
+gem 'flag-icons-rails', '~> 3.4'
+gem 'iso-639', '~> 0.3.6'
+
+# Custom API client
 gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'development'
-gem "flag-icons-rails", "~> 3.4"
-gem "iso-639", "~> 0.3.6"
+
+# Ruby 2.7.8 pinned gems (to remove when migrating to Ruby >= 3.0)
+gem 'ffi', '~> 1.16.3'
+gem 'net-ftp', '~> 0.2.0', require: false
+gem 'net-http', '~> 0.3.2'
 
 # Multi-Provider Authentication
 gem 'omniauth'
-gem "omniauth-rails_csrf_protection"
+gem 'omniauth-rails_csrf_protection'
 gem 'omniauth-github'
 gem 'omniauth-google-oauth2'
 gem 'omniauth-orcid'
 gem 'omniauth-keycloak'
 
 group :staging, :production, :appliance do
-  # application monitoring
+  # Application performance monitoring
   gem 'newrelic_rpm'
-  # logs in json format, useful for shipping logs to logstash
+
+  # Error monitoring
+  gem 'bugsnag', '~> 6.26'
+
+  # Logs in JSON format, useful for shipping logs to logstash
   # gem 'rackstash', git: 'https://github.com/planio-gmbh/rackstash.git'
   # gem 'logstash-logger'
 end
@@ -103,40 +129,49 @@ group :development do
   gem 'capistrano-rails', '~> 1.4', require: false
   gem 'capistrano-yarn', require: false
   gem 'ed25519', '>= 1.2', '< 2.0', require: false # https://github.com/miloserdow/capistrano-deploy/issues/42
-  gem 'html2haml'
-  gem 'listen'
-  # static code analysis
+
+  # Static code analysis
   gem 'brakeman', require: false
   gem 'rubocop', require: false
-  # gem 'i18n-debug'
+
+  # Haml support for Rails
+  gem 'haml-rails'
+  gem 'html2haml'
+
+  # Debugging tools
   # See https://guides.rubyonrails.org/debugging_rails_applications.html#debugging-with-the-debug-gem
-  gem 'debug', platforms: %i[ mri mingw x64_mingw ]
+  gem 'pry'
+  gem 'debug', platforms: %i[mri mingw x64_mingw]
 
-  # Use console on exceptions pages [https://github.com/rails/web-console]
+  # Use console on exceptions pages
+  # [https://github.com/rails/web-console]
   gem 'web-console'
+
+  # Internationalization tasks
+  # gem 'i18n-debug'
   gem 'i18n-tasks'
+  gem 'i18n-tasks-csv', '~> 1.1'
   gem 'deepl-rb'
-  gem 'letter_opener_web', '~> 2.0'
-  gem 'haml-rails'
-end
 
-group :test, :development do
-  gem 'rspec-rails'
+  # Email preview in the browser
+  gem 'letter_opener_web', '~> 2.0'
 end
 
 group :test do
-  # Use system testing [https://guides.rubyonrails.org/testing.html#system-testing]
+  # System testing
+  # [https://guides.rubyonrails.org/testing.html#system-testing]
   gem 'capybara'
+
+  # WebDriver for system testing
   gem 'selenium-webdriver'
+
+  # Code coverage generation
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
-  #gem 'webdrivers'
-end
-
-
-gem "net-ftp", "~> 0.2.0", require: false
-gem "net-http", "~> 0.3.2"
 
+  # Mock HTTP requests in tests
+  gem 'webmock'
 
-
-gem "bugsnag", "~> 6.26"
+  # Testing framework for Rails
+  gem 'rspec-rails'
+end