@@ -136,9 +136,19 @@ def tracked?(path)
     #
     # @return [Array<String>] list of absolute file paths
     def all_files
-      deleted_files = `git ls-files --deleted`.split(/\n/)
+      deleted_files, tracked_files = [%w[git ls-files --deleted], %w[git ls-files]].map do |command|
+        result = Overcommit::Utils.execute(command)
+        unless result.success?
+          raise Overcommit::Exceptions::Error,
+                "Error listing files. EXIT STATUS: #{result.status}.\n" \
+                "STDOUT: #{result.stdout}.\n" \
+                "STDERR: #{result.stderr}."
+        end
+
+        result.stdout.split(/\n/)
+      end
 
-      (`git ls-files`.split(/\n/) - deleted_files).
+      (tracked_files - deleted_files).
         map { |relative_file| File.expand_path(relative_file) }.
         reject { |file| File.directory?(file) } # Exclude submodule directories
     end
 
@@ -5,6 +5,49 @@
 describe 'overcommit --run' do
   subject { shell(%w[overcommit --run]) }
 
+  context 'when enumerating tracked files' do
+    around do |example|
+      repo do
+        echo({ 'PreCommit' => {
+          'ALL' => { 'enabled' => false },
+          'TrailingWhitespace' => {
+            'enabled' => true, 'on_warn' => 'fail', 'include' => ['**/*.rb']
+          }
+        } }.to_yaml, '.overcommit.yml')
+        example.run
+      end
+    end
+
+    it 'succeeds for a valid empty index' do
+      subject.status.should == 0
+    end
+
+    it 'fails for a tracked file with trailing whitespace' do
+      echo('puts :fixture ', 'normal.rb')
+      shell(%w[git add normal.rb]).status.should == 0
+      subject.status.should == 65
+    end
+
+    it 'ignores untracked files with trailing whitespace' do
+      echo('puts :fixture ', 'untracked.rb')
+      subject.status.should == 0
+    end
+
+    it 'ignores tracked files deleted from the working tree' do
+      echo('puts :fixture ', 'deleted.rb')
+      shell(%w[git add deleted.rb]).status.should == 0
+      FileUtils.rm('deleted.rb')
+      subject.status.should == 0
+    end
+
+    it 'fails instead of reporting success when the index is corrupt' do
+      File.binwrite('.git/index', 'invalid index')
+      subject.status.should_not == 0
+      (subject.stdout + subject.stderr).should include('Error listing files')
+      subject.stdout.should_not include('All pre-commit hooks passed')
+    end
+  end
+
   context 'when using an existing pre-commit hook script' do
     if Overcommit::OS.windows?
       let(:script_name) { 'test-script.bat' }
 
@@ -293,6 +293,37 @@
 
     it { should include(*%w[tracked staged].map { |file| File.expand_path(file) }) }
     it { should_not include File.expand_path('sub') }
+    it { should_not include File.expand_path('untracked') }
+
+    context 'when the index is empty' do
+      before { shell(%w[git read-tree --empty]).status.should == 0 }
+
+      it { should be_empty }
+    end
+
+    context 'when the index is unreadable' do
+      before { File.binwrite('.git/index', 'invalid index') }
+
+      it 'raises instead of returning an empty file list' do
+        expect { subject }.to raise_error(Overcommit::Exceptions::Error, /Error listing files/)
+      end
+
+      it 'includes the Git failure details' do
+        expect { subject }.to raise_error(Overcommit::Exceptions::Error, /STDERR: fatal:/)
+      end
+    end
+
+    context 'when listing tracked files fails after listing deleted files succeeds' do
+      before do
+        result = Overcommit::Subprocess::Result.new(128, '', 'fatal')
+        allow(Overcommit::Utils).to receive(:execute).and_call_original
+        allow(Overcommit::Utils).to receive(:execute).with(%w[git ls-files]).and_return(result)
+      end
+
+      it 'raises with the Git error' do
+        expect { subject }.to raise_error(Overcommit::Exceptions::Error, /STDERR: fatal/)
+      end
+    end
 
     context 'when a tracked file is deleted but the deletion is not staged' do
       around do |example|