Coder Upgrade ignores hidden files

Background:

Coder Upgrade processes files in files/coder_upgrade/old/ and creates a new copy in files/coder_upgrade/new/. When it encounters image files or files of unknown type, it simply copies the files unchanged, however it ignores any (.)hidden files in the old directory. This results in a loss of information and patches that look like:

Only in /var/www/drupal7/sites/default/files/coder_upgrade/old/openchurch_theme: .cvsignore
Only in /var/www/drupal7/sites/default/files/coder_upgrade/old/openchurch_theme: .gitignore
diff -up -r openchurch_theme.info openchurch_theme.info
--- openchurch_theme.info	2012-03-10 06:28:43.000000000 -0600
+++ openchurch_theme.info	2012-03-10 09:29:16.037147752 -0600

Offhand I can't think of a reason why this would be desirable.