[Bug #19892] Clean intermediate files regardless `-keep_temp`

Not to include such files in the result packages.

tool/make-snapshot

@@ -518,8 +518,7 @@ touch-unicode-files:
     end
     vcs.after_export(".") if exported
     clean.concat(Dir.glob("ext/**/autom4te.cache"))
-    FileUtils.rm_rf(clean) unless $keep_temp
-    FileUtils.rm_rf(".downloaded-cache")
+    clean.add(".downloaded-cache")
     if File.exist?("gems/bundled_gems")
       gems = Dir.glob("gems/*.gem")
       gems -= File.readlines("gems/bundled_gems").map {|line|
@@ -527,10 +526,11 @@ touch-unicode-files:
         name, version, _ = line.split(' ')
         "gems/#{name}-#{version}.gem"
       }
-      FileUtils.rm_f(gems)
+      clean.concat(gems)
     else
-      FileUtils.rm_rf("gems")
+      clean.add("gems")
     end
+    FileUtils.rm_rf(clean)
     if modified
       touch_all(modified, "**/*/", 0) do |name, stat|
         stat.mtime > modified