diff --git a/completion/bash-completion b/completion/bash-completion
index 2b587ea7..ae47746e 100644
--- a/completion/bash-completion
+++ b/completion/bash-completion
@@ -129,7 +129,7 @@ __complete_install() {
 __complete_update() {
 	opts="-h -c -v -q -b -i -I -e -w"
 	lopts="--help --createmeta --verbose --quiet --buildreport --interactive
- --icons --editor --wiki --pretty --clean"
+ --icons --editor --wiki --pretty --clean --delete-unknown"
 	case "${prev}" in
 		-e|--editor)
 			_filedir
diff --git a/fdroidserver/checkupdates.py b/fdroidserver/checkupdates.py
index 6b4831d4..c9405ad3 100644
--- a/fdroidserver/checkupdates.py
+++ b/fdroidserver/checkupdates.py
@@ -134,8 +134,8 @@ def check_tags(app, pattern):
 
             # Only process tags where the manifest exists...
             paths = common.manifest_paths(build_dir, flavour)
-            version, vercode, package = common.parse_androidmanifests(paths,
-                    app['Update Check Ignore'])
+            version, vercode, package = \
+                common.parse_androidmanifests(paths, app['Update Check Ignore'])
             if not package or package != appid or not version or not vercode:
                 continue
 
@@ -210,8 +210,8 @@ def check_repomanifest(app, branch=None):
 
         paths = common.manifest_paths(build_dir, flavour)
 
-        version, vercode, package = common.parse_androidmanifests(paths,
-                app['Update Check Ignore'])
+        version, vercode, package = \
+            common.parse_androidmanifests(paths, app['Update Check Ignore'])
         if not package:
             return (None, "Couldn't find package ID")
         if package != appid:
diff --git a/fdroidserver/update.py b/fdroidserver/update.py
index 8f189052..facd82da 100644
--- a/fdroidserver/update.py
+++ b/fdroidserver/update.py
@@ -884,6 +884,8 @@ def main():
     parser = OptionParser()
     parser.add_option("-c", "--createmeta", action="store_true", default=False,
                       help="Create skeleton metadata files that are missing")
+    parser.add_option("--delete-unknown", action="store_true", default=False,
+                      help="Delete APKs without metadata from the repo")
     parser.add_option("-v", "--verbose", action="store_true", default=False,
                       help="Spew out even more information than normal")
     parser.add_option("-q", "--quiet", action="store_true", default=False,
@@ -945,6 +947,45 @@ def main():
     if cc:
         cachechanged = True
 
+    # Generate warnings for apk's with no metadata (or create skeleton
+    # metadata files, if requested on the command line)
+    newmetadata = False
+    for apk in apks:
+        found = False
+        for app in apps:
+            if app['id'] == apk['id']:
+                found = True
+                break
+        if not found:
+            if options.createmeta:
+                f = open(os.path.join('metadata', apk['id'] + '.txt'), 'w')
+                f.write("License:Unknown\n")
+                f.write("Web Site:\n")
+                f.write("Source Code:\n")
+                f.write("Issue Tracker:\n")
+                f.write("Summary:" + apk['name'] + "\n")
+                f.write("Description:\n")
+                f.write(apk['name'] + "\n")
+                f.write(".\n")
+                f.close()
+                logging.info("Generated skeleton metadata for " + apk['id'])
+                newmetadata = True
+            else:
+                msg = apk['apkname'] + " (" + apk['id'] + ") has no metadata!"
+                if options.delete_unknown:
+                    logging.warn(msg + "\n\tdeleting: repo/" + apk['apkname'])
+                    rmf = os.path.join(repodirs[0], apk['apkname'])
+                    if not os.path.exists(rmf):
+                        logging.error("Could not find {0} to remove it".format(rmf))
+                    else:
+                        os.remove(rmf)
+                else:
+                    logging.warn(msg + "\n\tUse `fdroid update -c` to create it.")
+
+    # update the metadata with the newly created ones included
+    if newmetadata:
+        apps = metadata.read_metadata()
+
     # Scan the archive repo for apks as well
     if len(repodirs) > 1:
         archapks, cc = scan_apks(apps, apkcache, repodirs[1], knownapks)
@@ -997,35 +1038,6 @@ def main():
     # name comes from there!)
     apps = sorted(apps, key=lambda app: app['Name'].upper())
 
-    # Generate warnings for apk's with no metadata (or create skeleton
-    # metadata files, if requested on the command line)
-    for apk in apks:
-        found = False
-        for app in apps:
-            if app['id'] == apk['id']:
-                found = True
-                break
-        if not found:
-            if options.createmeta:
-                f = open(os.path.join('metadata', apk['id'] + '.txt'), 'w')
-                f.write("License:Unknown\n")
-                f.write("Web Site:\n")
-                f.write("Source Code:\n")
-                f.write("Issue Tracker:\n")
-                f.write("Summary:" + apk['name'] + "\n")
-                f.write("Description:\n")
-                f.write(apk['name'] + "\n")
-                f.write(".\n")
-                f.close()
-                logging.info("Generated skeleton metadata for " + apk['id'])
-            else:
-                logging.warn(apk['apkname'] + " (" + apk['id'] + ") has no metadata - removing")
-                rmf = os.path.join(repodirs[0], apk['apkname'])
-                if not os.path.exists(rmf):
-                    logging.error("Could not find {0} to remove it".format(rmf))
-                else:
-                    os.remove(rmf)
-
     if len(repodirs) > 1:
         archive_old_apks(apps, apks, archapks, repodirs[0], repodirs[1], config['archive_older'])