diff --git a/conan/api/conan_api.py b/conan/api/conan_api.py
index a3961ec967e..cc9b8c84dd4 100644
--- a/conan/api/conan_api.py
+++ b/conan/api/conan_api.py
@@ -61,6 +61,7 @@ def __init__(self, cache_folder=None):
 
     def reinit(self):
         self.config.reinit()
+        self.config.migrate()
         self.remotes.reinit()
         self.local.reinit()
 
diff --git a/conan/api/subapi/cache.py b/conan/api/subapi/cache.py
index 8c2dd089784..b3cf0b2159c 100644
--- a/conan/api/subapi/cache.py
+++ b/conan/api/subapi/cache.py
@@ -243,7 +243,6 @@ def get_backup_sources(self, package_list=None, exclude=True, only_upload=True):
         return download_cache.get_backup_sources_files(excluded_urls, package_list, only_upload)
 
 
-
 def _resolve_latest_ref(cache, ref):
     if ref.revision is None or ref.revision == "latest":
         ref.revision = None
diff --git a/conan/api/subapi/config.py b/conan/api/subapi/config.py
index dd1daf72f00..e1942c4928d 100644
--- a/conan/api/subapi/config.py
+++ b/conan/api/subapi/config.py
@@ -194,13 +194,12 @@ def appending_recursive_dict_update(d, u):
 
     def migrate(self):
         # Migration system
-        # TODO: Still needs refactoring - using it here for now for tests
+        # TODO: A prettier refactoring of migrators would be nice
         from conans.client.migrations import ClientMigrator
         migrator = ClientMigrator(self.home(), conan_version)
         migrator.migrate()
 
     def clean(self):
-        # TODO: Check what we're deleting
         contents = os.listdir(self.home())
         for content in contents:
             # keep packages
diff --git a/conan/cli/commands/config.py b/conan/cli/commands/config.py
index 0512a4db09b..8454d1401b3 100644
--- a/conan/cli/commands/config.py
+++ b/conan/cli/commands/config.py
@@ -140,9 +140,5 @@ def config_clean(conan_api, parser, subparser, *args):
     """
     Clean the configuration files in the Conan home folder. (Keeping installed packages)
     """
-    subparser.add_argument("-c", "--confirm", action='store_true',
-                           help="Do not request confirmation")
-    args = parser.parse_args(*args)
-    ui = UserInput(conan_api.config.get("core:non_interactive"))
-    if args.confirm or ui.request_boolean("Clear all configuration files?"):
-        conan_api.config.clean()
+    parser.parse_args(*args)
+    conan_api.config.clean()
diff --git a/test/integration/command/config_test.py b/test/integration/command/config_test.py
index 68ba1f4d0ec..a742ab06d54 100644
--- a/test/integration/command/config_test.py
+++ b/test/integration/command/config_test.py
@@ -211,7 +211,7 @@ def test_config_clean():
                   "extensions/compatibility/mycomp.py": "",
                   "extensions/commands/cmd_foo.py": "",
                   })
-    tc.run("config clean -c")
+    tc.run("config clean")
     tc.run("profile list")
     assert "foo" not in tc.out
     tc.run("remote list")