diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index b6bea464e23..2de7f246486 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -2766,7 +2766,8 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
                                                                      user=trans.user,
-                                                                     repository=repository )
+                                                                     repository=repository,
+                                                                     resetting_all_metadata_on_repository=True )
         rmm.reset_all_metadata_on_repository_in_tool_shed()
         rmm_metadata_dict = rmm.get_metadata_dict()
         rmm_invalid_file_tups = rmm.get_invalid_file_tups()
@@ -2787,7 +2788,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def reset_metadata_on_my_writable_repositories_in_tool_shed( self, trans, **kwd ):
-        rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user )
+        rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user, resetting_all_metadata_on_repository=True )
         if 'reset_metadata_on_selected_repositories_button' in kwd:
             message, status = rmm.reset_metadata_on_selected_repositories( **kwd )
         else:
diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py
index 81d5a62bdf9..0cf1fd40dc7 100644
--- a/lib/tool_shed/metadata/metadata_generator.py
+++ b/lib/tool_shed/metadata/metadata_generator.py
@@ -853,7 +853,7 @@ class MetadataGenerator( object ):
                             if tool_path and relative_install_dir:
                                 if relative_path_to_sample_file.startswith( os.path.join( tool_path, relative_install_dir ) ):
                                     relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :]
-                            sample_file_metadata_paths.append( relative_path_to_sample_file )
+                        sample_file_metadata_paths.append( relative_path_to_sample_file )
         return sample_file_metadata_paths, sample_file_copy_paths
 
     def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ):
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index f4166388731..5c7f8a5e7a1 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -834,7 +834,6 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
             if cloned_ok:
                 log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) )
                 self.set_changeset_revision( str( repo.changectx( changeset ) ) )
-                self.set_relative_install_dir( work_dir )
                 self.set_repository_files_dir( work_dir )
                 self.generate_metadata_for_changeset_revision()
                 if self.metadata_dict: