Fix infinite loop when collecting transitive excluded gems

lib/ruby_indexer/lib/ruby_indexer/configuration.rb

@@ -227,7 +227,10 @@ def initial_excluded_gems
       others.uniq!
       others.map!(&:name)
 
-      excluded.each do |dependency|
+      # Collect transitive dependencies in a separate array to avoid modifying `excluded` while iterating over it.
+      # Modifying an array during `.each` iteration causes Ruby to process newly added elements, which can lead to
+      # excessive iterations or infinite loops with circular dependencies. See: https://github.com/Shopify/ruby-lsp/issues/3912
+      transitive_excluded = excluded.each_with_object([]) do |dependency, acc|
         next unless dependency.runtime?
 
         spec = dependency.to_spec
@@ -236,14 +239,15 @@ def initial_excluded_gems
         spec.dependencies.each do |transitive_dependency|
           next if others.include?(transitive_dependency.name)
 
-          excluded << transitive_dependency
+          acc << transitive_dependency
         end
       rescue Gem::MissingSpecError
         # If a gem is scoped only to some specific platform, then its dependencies may not be installed either, but they
         # are still listed in dependencies. We can't index them because they are not installed for the platform, so we
         # just ignore if they're missing
       end
 
+      excluded.concat(transitive_excluded)
       excluded.uniq!
       excluded.map(&:name)
     rescue Bundler::GemfileNotFound