Decision Applier: Merge manual and system packages

This will enable merging manual added dependencies with
detected dependencies. This is usefull if a package will
be detected but e.g. license information is missing.
This change will use data from decision (homepage, approval, license)
and apply it to system package maching the manual one.
Currently manual decisions override the whole system package
which results in losing information (e.g. package_manager)

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)

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')]