diff -ru sks-1.1.4/common.ml sks-1.1.4.new/common.ml
--- sks-1.1.4/common.ml	2012-10-07 19:59:39.000000000 +0000
+++ sks-1.1.4.new/common.ml	2013-02-05 14:58:40.000000000 +0000
@@ -93,7 +93,7 @@
 
 let set_logfile extension =
   if !Settings.filelog then
-    let fname = (Filename.concat !Settings.basedir extension) ^ ".log" in
+    let fname = (Filename.concat !Settings.basedir "/var/log/sks/") ^ extension ^ ".log" in
     stored_logfile_name := Some fname;
     logfile := open_out_gen [ Open_wronly; Open_creat; Open_append; ]
       0o600 fname;
@@ -221,8 +221,8 @@
 let recon_address = !Settings.recon_address
 let http_port = !Settings.hkp_port
 let http_address = !Settings.hkp_address
-let db_command_name = Filename.concat !Settings.basedir "db_com_sock"
-let recon_command_name = Filename.concat !Settings.basedir "recon_com_sock"
+let db_command_name = Filename.concat !Settings.basedir "/var/run/sks/db_com_sock"
+let recon_command_name = Filename.concat !Settings.basedir "/var/run/sks/recon_com_sock"
 
 let db_command_addr = Unix.ADDR_UNIX db_command_name
 let recon_command_addr = Unix.ADDR_UNIX recon_command_name
diff -ru sks-1.1.4/dbserver.ml sks-1.1.4.new/dbserver.ml
--- sks-1.1.4/dbserver.ml	2012-10-07 19:59:39.000000000 +0000
+++ sks-1.1.4.new/dbserver.ml	2013-02-05 14:58:40.000000000 +0000
@@ -406,7 +406,7 @@
 
   let convert_web_fname fname =
     if verify_web_fname fname then
-      Filename.concat !Settings.basedir (Filename.concat "web" fname)
+      Filename.concat !Settings.basedir (Filename.concat "/var/lib/sks/www" fname)
     else raise (Wserver.Misc_error "Malformed requst")
 
   let supported_extensions =
diff -ru sks-1.1.4/getfileopts.ml sks-1.1.4.new/getfileopts.ml
--- sks-1.1.4/getfileopts.ml	2012-10-07 19:59:39.000000000 +0000
+++ sks-1.1.4.new/getfileopts.ml	2013-02-05 14:58:40.000000000 +0000
@@ -110,7 +110,7 @@
 (**************************************************************)
 (**************************************************************)
 
-let config_fname = "sksconf"
+let config_fname = "/etc/sks/sksconf"
 
 let parse args =
   Arg.current := 0;
diff -ru sks-1.1.4/reconserver.ml sks-1.1.4.new/reconserver.ml
--- sks-1.1.4/reconserver.ml	2012-10-07 19:59:39.000000000 +0000
+++ sks-1.1.4.new/reconserver.ml	2013-02-05 14:58:40.000000000 +0000
@@ -192,7 +192,7 @@
         let elements = ZSet.elements results in
         let hashes = hashconvert elements in
         print_hashes (sockaddr_to_string http_addr) hashes;
-        log_diffs (sprintf "diff-%s.txt" (sockaddr_to_name http_addr)) hashes;
+        log_diffs (sprintf "/var/spool/sks/diff-%s.txt" (sockaddr_to_name http_addr)) hashes;
         if List.length elements > 0
         then
           begin
@@ -229,7 +229,7 @@
         plerror 4 "Reconciliation complete";
         let hashes = hashconvert results in
         print_hashes (sockaddr_to_string http_addr) hashes;
-        log_diffs (sprintf "diff-%s.txt" (sockaddr_to_name http_addr)) hashes;
+        log_diffs (sprintf "/var/spool/sks/diff-%s.txt" (sockaddr_to_name http_addr)) hashes;
         match results with
             [] -> []
           | _ ->
diff -ru sks-1.1.4/settings.ml sks-1.1.4.new/settings.ml
--- sks-1.1.4/settings.ml	2012-10-07 19:59:39.000000000 +0000
+++ sks-1.1.4.new/settings.ml	2013-02-05 14:58:40.000000000 +0000
@@ -200,7 +200,7 @@
 let command_timeout = ref 60
 let set_command_timeout value = command_timeout := value
 
-let sendmail_cmd = ref "sendmail -t -oi"
+let sendmail_cmd = ref "/usr/lib/sendmail -t -oi"
 let set_sendmail_cmd value = sendmail_cmd := value
 
 let membership_reload_time = ref (60. *. 60. *. 6.)
@@ -226,15 +226,15 @@
 
 let use_stdin = ref false
 
-let basedir = ref "."
+let basedir = ref ""
 
-let base_dbdir = "KDB"
-let base_ptree_dbdir = "PTree"
-let base_membership_file = "membership"
-let base_mailsync_file = "mailsync"
-let base_dumpdir = "dump"
-let base_msgdir = "messages"
-let base_failed_msgdir = "failed_messages"
+let base_dbdir = "/var/lib/sks/DB"
+let base_ptree_dbdir = "/var/lib/sks/PTree"
+let base_membership_file = "/etc/sks/membership"
+let base_mailsync_file = "/etc/sks/mailsync"
+let base_dumpdir = "/var/lib/sks/dump"
+let base_msgdir = "/var/spool/sks/messages"
+let base_failed_msgdir = "/var/spool/sks/failed_messages"
 
 let dbdir = lazy (Filename.concat !basedir base_dbdir)
 let ptree_dbdir = lazy (Filename.concat !basedir base_ptree_dbdir)
@@ -290,7 +290,7 @@
     ("-hkp_address",Arg.String set_hkp_address, " Set hkp binding address");
     ("-use_port_80",Arg.Set use_port_80,
      " Have the HKP interface listen on port 80, as well as the hkp_port");
-    ("-basedir", Arg.Set_string basedir, " Base directory");
+    ("-basedir", Arg.Set_string basedir, " Base directory (Take special care if running the Debian package!)");
     ("-stdoutlog", Arg.Clear filelog,
      " Send log messages to stdout instead of log file");
     ("-diskptree", Arg.Set disk_ptree,