commit 805859f4a75d5d8118d9a307ee296efe1d9cff2f
Author: Jaroslav Mracek <jmracek@redhat.com>
Date:   Mon Sep 24 14:31:26 2018 +0200

    Exclude system and commandline pkg from filtering (RhBug:1630226)
    
    https://bugzilla.redhat.com/show_bug.cgi?id=1630226

diff --git a/dnf/base.py b/dnf/base.py
index 1c41af7a..34ea864e 100644
--- a/dnf/base.py
+++ b/dnf/base.py
@@ -294,6 +294,8 @@ class Base(object):
 
         # collect all hotfix repo repoids - we don't filter them at all
         hotfix_repos = [i.id for i in self.repos.iter_enabled() if i.hotfixes]
+        hotfix_repos.append(hawkey.SYSTEM_REPO_NAME)
+        hotfix_repos.append(hawkey.CMDLINE_REPO_NAME)
 
         # collect all RPM $names for bare RPMs filtering
         names = {hawkey.split_nevra(i).name for i in include_nevras_set}