Package: iceweasel Version: 46.0~a2+20160217064514-1 You need to reverse the order of steps, and also remove empty directories, and more files, to avoid the user getting these messages.
Unpacking iceweasel (46.0~a2+20160217064514-1) over (45.0~a2+20160107004004-1) ... dpkg: warning: unable to delete old directory '/etc/iceweasel/profile/chrome': Directory not empty dpkg: warning: unable to delete old directory '/etc/iceweasel/profile': Directory not empty Soon after I then do $ find /etc/iceweasel/ -ls 132855 4 drwxr-xr-x 5 root root 4096 7月 27 2013 /etc/iceweasel/ 132858 4 drwxr-xr-x 3 root root 4096 3月 1 07:23 /etc/iceweasel/profile 132863 4 -rw-r--r-- 1 root root 473 7月 26 2013 /etc/iceweasel/profile/prefs.js.dpkg-remove 132865 4 -rw-r--r-- 1 root root 366 7月 26 2013 /etc/iceweasel/profile/localstore.rdf.dpkg-remove 132860 4 drwxr-xr-x 2 root root 4096 3月 1 07:23 /etc/iceweasel/profile/chrome 132862 4 -rw-r--r-- 1 root root 761 7月 26 2013 /etc/iceweasel/profile/chrome/userContent-example.css.dpkg-remove 132861 4 -rw-r--r-- 1 root root 1165 7月 26 2013 /etc/iceweasel/profile/chrome/userChrome-example.css.dpkg-remove 132859 4 -rw-r--r-- 1 root root 569 7月 26 2013 /etc/iceweasel/profile/mimeTypes.rdf.dpkg-remove 132856 4 drwxr-xr-x 2 root root 4096 3月 1 07:23 /etc/iceweasel/pref 133364 4 -rw-r--r-- 1 root root 1219 2月 18 15:30 /etc/iceweasel/pref/iceweasel.js.dpkg-new 133140 4 -rw-r--r-- 1 root root 1219 9月 7 17:36 /etc/iceweasel/pref/iceweasel.js 132866 4 drwxr-xr-x 4 root root 4096 7月 27 2013 /etc/iceweasel/searchplugins 132876 4 drwxr-xr-x 2 root root 4096 3月 1 07:23 /etc/iceweasel/searchplugins/common 133365 4 -rw-r--r-- 1 root root 1245 2月 18 12:07 /etc/iceweasel/searchplugins/common/debsearch.xml.dpkg-new 132878 4 -rw-r--r-- 1 root root 1245 7月 26 2013 /etc/iceweasel/searchplugins/common/debsearch.xml 132867 4 drwxr-xr-x 3 root root 4096 7月 27 2013 /etc/iceweasel/searchplugins/locale 132868 4 drwxr-xr-x 2 root root 4096 9月 9 07:00 /etc/iceweasel/searchplugins/locale/en-US A little later I do it again $ find /etc/iceweasel/ -ls 132855 4 drwxr-xr-x 5 root root 4096 7月 27 2013 /etc/iceweasel/ 132858 4 drwxr-xr-x 3 root root 4096 3月 1 07:30 /etc/iceweasel/profile 132860 4 drwxr-xr-x 2 root root 4096 3月 1 07:30 /etc/iceweasel/profile/chrome 132856 4 drwxr-xr-x 2 root root 4096 3月 1 07:30 /etc/iceweasel/pref 133140 4 -rw-r--r-- 1 root root 1219 9月 7 17:36 /etc/iceweasel/pref/iceweasel.js 132866 4 drwxr-xr-x 4 root root 4096 7月 27 2013 /etc/iceweasel/searchplugins 132876 4 drwxr-xr-x 2 root root 4096 3月 1 07:30 /etc/iceweasel/searchplugins/common 132878 4 -rw-r--r-- 1 root root 1245 7月 26 2013 /etc/iceweasel/searchplugins/common/debsearch.xml 132867 4 drwxr-xr-x 3 root root 4096 7月 27 2013 /etc/iceweasel/searchplugins/locale 132868 4 drwxr-xr-x 2 root root 4096 9月 9 07:00 /etc/iceweasel/searchplugins/locale/en-US One also sees Setting up iceweasel (46.0~a2+20160217064514-1) ... Removing obsolete conffile /etc/iceweasel/profile/chrome/userChrome-example.css ... Removing obsolete conffile /etc/iceweasel/profile/chrome/userContent-example.css ... Removing obsolete conffile /etc/iceweasel/profile/localstore.rdf ... Removing obsolete conffile /etc/iceweasel/profile/mimeTypes.rdf ... Removing obsolete conffile /etc/iceweasel/profile/prefs.js ...

