diff --git a/src/omero/cli.py b/src/omero/cli.py
index 976e56413..e6503fd25 100755
--- a/src/omero/cli.py
+++ b/src/omero/cli.py
@@ -1646,7 +1646,7 @@ def loadplugins(self):
 
     def loadpath(self, pathobj):
         if pathobj.isdir():
-            for plugin in pathobj.walkfiles("*.py"):
+            for plugin in sorted(pathobj.walkfiles("*.py")):
                 if -1 == plugin.find("#"):  # Omit emacs files
                     self.loadpath(path(plugin))
         else:
diff --git a/src/omero/plugins/metadata.py b/src/omero/plugins/_metadata_deprecated.py
similarity index 96%
rename from src/omero/plugins/metadata.py
rename to src/omero/plugins/_metadata_deprecated.py
index b5a2ca290..496337aa3 100755
--- a/src/omero/plugins/metadata.py
+++ b/src/omero/plugins/_metadata_deprecated.py
@@ -40,6 +40,10 @@
 GUI clients.
 """
 
+DEPRECATION_MESSAGE = (
+    "This plugin is deprecated as of OMERO 5.4.8. Use the plugin"
+    " available from https://pypi.org/project/omero-metadata/"
+    " instead.")
 
 ANNOTATION_TYPES = [t for t in dir(omero.model)
                     if re.match(r'[A-Za-z0-9]+Annotation$', t)]
@@ -285,6 +289,7 @@ def _format_ann(self, md, obj, indent=None):
 
     def summary(self, args):
         "Provide a general summary of available metadata"
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         name = md.get_name()
         line = "-" * len(name)
@@ -332,6 +337,7 @@ def summary(self, args):
 
     def original(self, args):
         "Print the original metadata in ini format"
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         try:
             source, global_om, series_om = md.get_original()
@@ -370,6 +376,7 @@ def _output_ann(self, mdobj, func, parents, indent):
     def bulkanns(self, args):
         ("Provide a list of the NSBULKANNOTATION tables linked "
          "to the given object")
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         indent = None
         if args.report:
@@ -380,6 +387,7 @@ def bulkanns(self, args):
     def measures(self, args):
         ("Provide a list of the NSMEASUREMENT tables linked "
          "to the given object")
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         indent = None
         if args.report:
@@ -394,7 +402,7 @@ def get_anns(md):
                 if args.nsre and not re.match(args.nsre, a.get_ns()):
                     continue
                 yield a
-
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         indent = None
         if args.report:
@@ -408,7 +416,7 @@ def get_anns(md):
                 if args.nsre and not re.match(args.nsre, a.get_ns()):
                     continue
                 yield a
-
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         indent = None
         if args.report:
@@ -417,6 +425,7 @@ def get_anns(md):
 
     def testtables(self, args):
         "Tests whether tables can be created and initialized"
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         client, conn = self._clientconn(args)
 
         sf = client.getSession()
@@ -449,6 +458,7 @@ def testtables(self, args):
 
     def populate(self, args):
         "Add metadata (bulk-annotations) to an object"
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         client, conn = self._clientconn(args)
         # TODO: Configure logging properly
@@ -500,6 +510,7 @@ def populate(self, args):
 
     def rois(self, args):
         "Manage ROIs"
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         if args.delete:
             graphspec = "/%s/Roi:%d" % (md.get_type(), md.get_id())
@@ -545,6 +556,7 @@ def rois(self, args):
 
     def populateroi(self, args):
         "Add ROIs to an object"
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         md = self._load(args)
         client = self.ctx.conn(args)
         # TODO: Configure logging properly
@@ -574,6 +586,7 @@ def populateroi(self, args):
 
     def pixelsize(self, args):
         "Set physical pixel size"
+        self.ctx.err(DEPRECATION_MESSAGE, DeprecationWarning)
         if not args.x and not args.y and not args.z:
             self.ctx.die(100, "No pixel sizes specified.")
 
@@ -635,11 +648,7 @@ def pixelsize(self, args):
 
 try:
     if "OMERO_DEV_PLUGINS" in os.environ:
-        warnings.warn(
-            "This module is deprecated as of OMERO 5.4.8. Use the metadata"
-            " CLI plugin available from"
-            " https://pypi.org/project/omero-metadata/ instead.",
-            DeprecationWarning)
+        warnings.warn(DEPRECATION_MESSAGE, DeprecationWarning)
         register("metadata", MetadataControl, HELP)
 except NameError:
     if __name__ == "__main__":
diff --git a/src/omero/plugins/upload.py b/src/omero/plugins/_upload_deprecated.py
similarity index 94%
rename from src/omero/plugins/upload.py
rename to src/omero/plugins/_upload_deprecated.py
index 022085afd..94e0ded1e 100755
--- a/src/omero/plugins/upload.py
+++ b/src/omero/plugins/_upload_deprecated.py
@@ -53,7 +53,7 @@ def _configure(self, parser):
     def upload(self, args):
         self.ctx.err(
             "This module is deprecated as of OMERO 5.5.0. Use the module"
-            " available from https://pypi.org/project/omero-cli-upload/"
+            " available from https://pypi.org/project/omero-upload/"
             " instead.", DeprecationWarning)
         client = self.ctx.conn(args)
         objIds = []
@@ -76,7 +76,7 @@ def upload(self, args):
         warnings.warn(
             "This plugin is deprecated as of OMERO 5.5.0. Use the upload"
             " CLI plugin available from"
-            " https://pypi.org/project/omero-cli-upload/ instead.",
+            " https://pypi.org/project/omero-upload/ instead.",
             DeprecationWarning)
         register("upload", UploadControl, HELP)
 except NameError: