Fix yarn berry security updates resolving to latest instead of target version (#15091)

* Implement Yarn Berry security update handling and add corresponding tests
* Refactor Yarn Berry version handling to ensure correct version pinning during updates

Author: kbukum1

npm_and_yarn/lib/dependabot/npm_and_yarn/file_updater/berry_lockfile_handler.rb

@@ -0,0 +1,108 @@
+# typed: strict
+# frozen_string_literal: true
+
+require "sorbet-runtime"
+require "yaml"
+
+require "dependabot/npm_and_yarn/file_updater"
+
+# Handles yarn berry lockfile manipulation — parsing descriptors, finding
+# entries, and rewriting keys from exact versions back to ranges. This is
+# the berry equivalent of yarn classic's replace-lockfile-declaration.ts.
+module Dependabot
+  module NpmAndYarn
+    class FileUpdater < Dependabot::FileUpdaters::Base
+      class BerryLockfileHandler
+        extend T::Sig
+
+        # Parses a yarn berry lockfile (YAML format). Returns nil if unparseable.
+        sig { params(lockfile_path: String).returns(T.nilable(T::Hash[String, T.untyped])) }
+        def self.parse(lockfile_path)
+          return unless File.exist?(lockfile_path)
+
+          parsed = YAML.safe_load_file(lockfile_path)
+          parsed.is_a?(Hash) ? parsed : nil
+        end
+
+        # Checks if the parsed lockfile has the target version for a dependency.
+        sig { params(parsed: T::Hash[String, T.untyped], dep_name: String, version: String).returns(T::Boolean) }
+        def self.version_matches?(parsed, dep_name, version)
+          parsed.any? do |key, value|
+            next false unless value.is_a?(Hash)
+
+            key.to_s.split(", ").any? { |part| split_descriptor(part)[0] == dep_name } &&
+              value["version"] == version
+          end
+        end
+
+        # Rewrites a lockfile descriptor key from exact version to range.
+        # Example: "axios@npm:1.15.2" → "axios@npm:^1.15.2"
+        # The resolved version, checksum, and dependencies remain unchanged.
+        sig do
+          params(
+            lockfile_path: String,
+            dep_name: String,
+            version: String,
+            requirement: String
+          ).void
+        end
+        def self.replace_declaration(lockfile_path, dep_name, version, requirement)
+          return unless File.exist?(lockfile_path)
+
+          content = File.read(lockfile_path)
+          parsed = parse(lockfile_path)
+          return unless parsed
+
+          exact_key = find_exact_key(parsed, dep_name, version)
+          return unless exact_key
+
+          protocol = extract_protocol(exact_key, dep_name)
+          new_key = "#{dep_name}@#{protocol}#{requirement}"
+
+          escaped = Regexp.escape(exact_key)
+          File.write(lockfile_path, content.gsub(/^"#{escaped}":/m, "\"#{new_key}\":"))
+        end
+
+        # Finds the lockfile key containing the given dep name with exact version.
+        # Handles composite keys (e.g., "a@npm:1.0, a@npm:^1.0").
+        sig { params(parsed: T::Hash[String, T.untyped], dep_name: String, version: String).returns(T.nilable(String)) }
+        def self.find_exact_key(parsed, dep_name, version)
+          parsed.keys.find do |key|
+            next false unless key.is_a?(String)
+
+            key.split(", ").any? do |part|
+              name, desc = split_descriptor(part)
+              name == dep_name && (desc&.end_with?(version) || false)
+            end
+          end
+        end
+
+        # Splits a yarn berry descriptor into [package_name, version/range].
+        # Handles scoped packages like @scope/pkg@npm:^1.0.0.
+        sig { params(descriptor: String).returns([String, T.nilable(String)]) }
+        def self.split_descriptor(descriptor)
+          if descriptor.start_with?("@")
+            at_index = descriptor.index("@", 1)
+            return [descriptor, nil] unless at_index
+
+            [T.must(descriptor[0...at_index]), descriptor[(at_index + 1)..]]
+          else
+            parts = descriptor.split("@", 2)
+            [T.must(parts[0]), parts[1]]
+          end
+        end
+
+        # Extracts the protocol prefix (e.g., "npm:") from a descriptor.
+        sig { params(key: String, dep_name: String).returns(String) }
+        def self.extract_protocol(key, dep_name)
+          part = key.split(", ").find { |p| split_descriptor(p)[0] == dep_name }
+          return "" unless part
+
+          _, descriptor = split_descriptor(part)
+          match = descriptor&.match(/^([a-z]+:)/)
+          match ? T.must(match[1]) : ""
+        end
+      end
+    end
+  end
+end

npm_and_yarn/lib/dependabot/npm_and_yarn/file_updater/yarn_lockfile_updater.rb

@@ -21,6 +21,7 @@ class YarnLockfileUpdater
         require_relative "npmrc_builder"
         require_relative "package_json_updater"
         require_relative "package_json_preparer"
+        require_relative "berry_lockfile_handler"
 
         extend T::Sig
 
@@ -222,6 +223,13 @@ def run_yarn_berry_top_level_updater(top_level_dependency_updates:, yarn_lock:)
 
           if top_level_dependency_updates.all? { |dep| requirements_changed?(dep[:name]) }
             Helpers.run_yarn_command("install #{yarn_berry_args}".strip)
+
+            # Yarn berry resolves ranges to the latest matching version, which
+            # may differ from Dependabot's target. If the lockfile resolved to a
+            # different version, re-install with the exact target and rewrite
+            # the lockfile descriptor back to the range — same approach as yarn
+            # classic's replaceLockfileDeclaration.
+            pin_berry_versions_if_needed(top_level_dependency_updates, yarn_lock)
           else
             updates = top_level_dependency_updates.collect do |dep|
               dep[:name]
@@ -243,6 +251,78 @@ def requirements_changed?(dependency_name)
           dep.requirements != dep.previous_requirements
         end
 
+        # Checks if yarn resolved to a different version than Dependabot's target
+        # and re-pins if needed. Yarn berry resolves ranges to the latest matching
+        # version, which can bypass Dependabot's version selection — including
+        # security updates (minimum safe version), ignore conditions, and cooldown.
+        sig do
+          params(
+            top_level_dependency_updates: T::Array[T::Hash[Symbol, T.untyped]],
+            yarn_lock: Dependabot::DependencyFile
+          ).void
+        end
+        def pin_berry_versions_if_needed(top_level_dependency_updates, yarn_lock)
+          parsed = BerryLockfileHandler.parse(yarn_lock.name)
+          return unless parsed
+
+          top_level_dependency_updates.each do |dep|
+            pin_berry_version_if_needed(dep, yarn_lock, parsed)
+          end
+        end
+
+        sig do
+          params(
+            dep: T::Hash[Symbol, T.untyped],
+            yarn_lock: Dependabot::DependencyFile,
+            parsed_lockfile: T::Hash[String, T.untyped]
+          ).void
+        end
+        def pin_berry_version_if_needed(dep, yarn_lock, parsed_lockfile)
+          version = dep[:version]
+          return unless version
+
+          dep_name = T.cast(dep[:name], String)
+          reqs = dep[:requirements]
+          return if reqs.nil? || reqs.empty?
+          return if reqs.any? { |req| req[:source] && req[:source][:type] == "git" }
+          return if BerryLockfileHandler.version_matches?(parsed_lockfile, dep_name, T.cast(version, String))
+
+          saved_package_jsons = save_package_jsons
+
+          Helpers.run_yarn_command(
+            "up #{dep_name}@#{version} #{yarn_berry_args}".strip,
+            fingerprint: "up <dep>@<version> #{yarn_berry_args}".strip
+          )
+
+          reqs.each do |req|
+            requirement = req[:requirement]
+            next unless requirement
+
+            BerryLockfileHandler.replace_declaration(yarn_lock.name, dep_name, T.cast(version, String), requirement)
+          end
+
+          # Restore package.json and re-install to normalize lockfile descriptors,
+          # same as yarn classic's replaceLockfileDeclaration flow.
+          restore_package_jsons(saved_package_jsons)
+          Helpers.run_yarn_command("install #{yarn_berry_args}".strip)
+        end
+
+        sig { returns(T::Hash[String, String]) }
+        def save_package_jsons
+          result = T.let({}, T::Hash[String, String])
+          package_files.each do |file|
+            next unless File.exist?(file.name)
+
+            result[file.name] = File.read(file.name)
+          end
+          result
+        end
+
+        sig { params(saved: T::Hash[String, String]).void }
+        def restore_package_jsons(saved)
+          saved.each { |path, content| File.write(path, content) }
+        end
+
         sig { params(yarn_lock: Dependabot::DependencyFile).returns(T::Hash[String, String]) }
         def run_yarn_berry_subdependency_updater(yarn_lock:)
           dep = T.must(sub_dependencies.first)