Improve `Gitlab::EeCompatCheck` by using the `git apply --3way` flag

This should solve 99% of the false-positive of the `ee_compat_check` job.

lib/gitlab/ee_compat_check.rb

@@ -119,7 +119,7 @@ module Gitlab
       step("Reseting to latest master", %w[git reset --hard origin/master])
       step("Checking if #{patch_path} applies cleanly to EE/master")
-      output, status = Gitlab::Popen.popen(%W[git apply --check #{patch_path}])
+      output, status = Gitlab::Popen.popen(%W[git apply --check --3way #{patch_path}])
       unless status.zero?
         failed_files = output.lines.reduce([]) do |memo, line|