diff --git a/pubs/config/spec.py b/pubs/config/spec.py
index 699a26d..27cf449 100644
--- a/pubs/config/spec.py
+++ b/pubs/config/spec.py
@@ -71,6 +71,14 @@ pages     = string(default='')
 # comma-separated list of the plugins to load
 active = list(default=list())
 
+[[alias]]
+# new subcommands can be defined, e.g.:
+# print = open --with lp
+# evince = open --with evince
+
+# shell commands can also be defined, by prefixing them with a bang `!`, e.g:
+# count = !pubs list -k | wc -l
+
 [internal]
 # The version of this configuration file. Do not edit.
 version = string(min=5, default='{}')
diff --git a/pubs/pubs_cmd.py b/pubs/pubs_cmd.py
index 3193b61..b791234 100644
--- a/pubs/pubs_cmd.py
+++ b/pubs/pubs_cmd.py
@@ -33,15 +33,15 @@ CORE_CMDS = collections.OrderedDict([
 
 def execute(raw_args=sys.argv):
 
-    conf_parser = argparse.ArgumentParser(add_help=False)
+    conf_parser = argparse.ArgumentParser(prog="pubs", add_help=False)
     conf_parser.add_argument("-c", "--config", help="path to config file",
                              type=str, metavar="FILE")
-    conf_parser.add_argument("-u", "--update", help="update config if needed",
-                             default=False, action='store_true')
-    args, remaining_args = conf_parser.parse_known_args(raw_args[1:])
+    #conf_parser.add_argument("-u", "--update", help="update config if needed",
+    #                         default=False, action='store_true')
+    top_args, remaining_args = conf_parser.parse_known_args(raw_args[1:])
 
-    if args.config:
-        conf_path = args.config
+    if top_args.config:
+        conf_path = top_args.config
     else:
         conf_path = config.get_confpath(verify=False)  # will be checked on load
 
@@ -49,7 +49,7 @@ def execute(raw_args=sys.argv):
     if len(remaining_args) > 0 and remaining_args[0] != 'init':
         try:
             conf = config.load_conf(path=conf_path, check=False)
-            if args.update and update.update_check(conf, path=conf.filename):
+            if update.update_check(conf, path=conf.filename):
                 # an update happened, reload conf.
                 conf = config.load_conf(path=conf_path, check=False)
             config.check_conf(conf)
@@ -81,4 +81,5 @@ def execute(raw_args=sys.argv):
 
     # Parse and run appropriate command
     args = parser.parse_args(remaining_args)
+    args.prog = "pubs" # FIXME?
     args.func(conf, args)
diff --git a/pubs/update.py b/pubs/update.py
index 2a31aba..aab8879 100644
--- a/pubs/update.py
+++ b/pubs/update.py
@@ -69,7 +69,7 @@ def update(conf, code_version, repo_version, path=None):
         return True
 
     # continuous update while configuration is stabilizing
-    if repo_version == code_version == ['0', '6', '0']:
+    if repo_version == ['0', '6', '0'] and repo_version < code_version:
         default_conf = config.load_default_conf()
         for section_name, section in conf.items():
             for key, value in section.items():
@@ -78,6 +78,10 @@ def update(conf, code_version, repo_version, path=None):
                     default_conf[section_name][key] = value
                 except KeyError:
                     pass
+        # we don't update plugins
+        for section_name, section in conf['plugins'].items():
+            default_conf[section_name]['plugins'][section_name] = section
+
 
         # comparing potential changes
         with open(path, 'r') as f:
@@ -85,7 +89,6 @@ def update(conf, code_version, repo_version, path=None):
         new_conf_text = io.BytesIO()
         default_conf.write(outfile=new_conf_text)
 
-
         if new_conf_text.getvalue() != old_conf_text:
 
             backup_path = path + '.old'
diff --git a/readme.md b/readme.md
index cc0aaa1..9409f46 100644
--- a/readme.md
+++ b/readme.md
@@ -52,16 +52,16 @@ This ensure that your reference file is always up-to-date; you can cite a paper
 
 and then add `\cite{Loeb_2012}` in your manuscript. After running the bash script, the citation will correctly appear in your compiled pdf.
 
-Customization
--------------
-Pubs is designed to interact well with your command line tool chain. You can add custom commands to pubs by defining aliases in your config file. Here are a few examples.
+## Customization
 
-    [alias]
-    print = open -w lp
-    count = !pubs list -k | wc -l
+Pubs is designed to interact well with your command line tool chain. You can add custom commands to pubs by defining aliases in your config file.
 
-For more advanced functionalities, pubs also support plugins. Actually *alias* is itself a plugin!
+    [[alias]]
+    evince = open --with evince
+    count = !pubs list -k | wc -l
 
+The first command defines a new subcommand: `pubs open -w lp` will be executed when `pubs print` is typed.
+The second starts with a bang: `!`, and is treated as a shell command.
 
 ## Requirements