diff --git a/lib/license_finder/decision_applier.rb b/lib/license_finder/decision_applier.rb
index 4a401cd69..e0e3d2e27 100644
--- a/lib/license_finder/decision_applier.rb
+++ b/lib/license_finder/decision_applier.rb
@@ -4,7 +4,7 @@ module LicenseFinder
   class DecisionApplier
     def initialize(options)
       @decisions = options.fetch(:decisions)
-      @all_packages = decisions.packages + options.fetch(:packages)
+      @all_packages = options.fetch(:packages).to_set + @decisions.packages.to_set
       @acknowledged = apply_decisions
     end
 
@@ -28,10 +28,14 @@ def any_packages?
 
     def apply_decisions
       all_packages
-        .map { |package| with_decided_licenses(package) }
-        .map { |package| with_approval(package) }
-        .map { |package| with_homepage(package) }
         .reject { |package| ignored?(package) }
+        .map do |package|
+          with_homepage(
+            with_approval(
+              with_decided_licenses(package)
+            )
+          )
+        end
     end
 
     def ignored?(package)
diff --git a/spec/lib/license_finder/decision_applier_spec.rb b/spec/lib/license_finder/decision_applier_spec.rb
index b6c08912f..00aa793fa 100644
--- a/spec/lib/license_finder/decision_applier_spec.rb
+++ b/spec/lib/license_finder/decision_applier_spec.rb
@@ -14,6 +14,15 @@ module LicenseFinder
 
     describe '#acknowledged' do
       it 'combines manual and system packages' do
+        decision_applier = described_class.new(
+          decisions: Decisions.new.add_package('system', nil).license('system', 'MIT'),
+          packages: [Package.new('system', '1.0.0')]
+        )
+        package = decision_applier.acknowledged.first
+        expect([package.name, package.version, package.licenses.first.name]).to match_array %w[system 1.0.0 MIT]
+      end
+
+      it 'merges manual packages with system packages' do
         decision_applier = described_class.new(
           decisions: Decisions.new.add_package('manual', nil),
           packages: [Package.new('system')]