webapp checkout contains Untracked/deleted files

root@elephant:/srv/leap/webapp# git status
# Not currently on any branch.
# Changes not staged for commit:
#   (use "git add/rm ..." to update what will be committed)
#   (use "git checkout -- ..." to discard changes in working directory)
#
#	deleted:    config/customization/README.md
#
# Untracked files:
#   (use "git add ..." to include in what will be committed)
#
#	config/customization/locales/
#	config/customization/public/
#	config/customization/stylesheets/
#	config/customization/views/
#	config/provider/

root@wallaby:/srv/leap/webapp# git status
# Not currently on any branch.
# Changes not staged for commit:
#   (use "git add/rm ..." to update what will be committed)
#   (use "git checkout -- ..." to discard changes in working directory)
#
#	deleted:    config/customization/README.md
#
# Untracked files:
#   (use "git add ..." to include in what will be committed)
#
#	config/couchdb.yml_admin
#	config/customization/locales/
#	config/customization/public/
#	config/customization/stylesheets/
#	config/customization/views/
#	config/provider/

(from redmine: created on 2014-01-13, closed on 2014-02-07)