diff --git a/lib/suma/collection_manifest.rb b/lib/suma/collection_manifest.rb
index 8b3cbd3..8f358d5 100644
--- a/lib/suma/collection_manifest.rb
+++ b/lib/suma/collection_manifest.rb
@@ -91,7 +91,7 @@ def expand_schemas_only(schema_output_path)
         CollectionManifest.new(
           identifier: schema.id,
           title: schema.id,
-          file: File.join(schema_output_path, "doc_#{schema.id}", fname),
+          file: File.join(schema_output_path, schema.id, "doc_#{fname}"),
           # schema_source: schema.path
         )
       end
@@ -113,5 +113,12 @@ def expand_schemas_only(schema_output_path)
 
       [self, added]
     end
+
+    def remove_schemas_only_sources
+      ret = entry.each_with_object([]) do |e, m|
+        e.schemas_only or m << e
+      end
+      self.entry = ret
+    end
   end
 end
diff --git a/lib/suma/processor.rb b/lib/suma/processor.rb
index fffabf0..1553fc9 100644
--- a/lib/suma/processor.rb
+++ b/lib/suma/processor.rb
@@ -23,7 +23,7 @@ def run(metanorma_yaml_path:, schemas_all_path:, compile:, output_directory: "_s
         collection_config_path = site_config.metanorma.source.files.first
         collection_config = Suma::CollectionConfig.from_file(collection_config_path)
         collection_config.path = collection_config_path
-        collection_config.manifest.expand_schemas_only("plain_schemas")
+        collection_config.manifest.expand_schemas_only("schema_docs")
 
         exported_schema_config = collection_config.manifest.export_schema_config(schemas_all_path)
         exported_schema_config.path = schemas_all_path
@@ -32,6 +32,8 @@ def run(metanorma_yaml_path:, schemas_all_path:, compile:, output_directory: "_s
         exported_schema_config.to_file
         Utils.log "Done."
 
+        # now get rid of the source documents for schema sources
+
         col = Suma::SchemaCollection.new(
           config_yaml: schemas_all_path,
           manifest: collection_config.manifest,
@@ -46,6 +48,10 @@ def run(metanorma_yaml_path:, schemas_all_path:, compile:, output_directory: "_s
           Utils.log "No compile option set. Skipping schema compilation."
         end
 
+        new_collection_config_path = "collection-output.yaml"
+        collection_config.manifest.remove_schemas_only_sources
+        collection_config.to_file(new_collection_config_path)
+
         # TODO: Do we still need this?
         # Define Proc to resolve fileref
         my_fileref_proc = proc do |ref_folder, fileref|
@@ -86,7 +92,7 @@ def run(metanorma_yaml_path:, schemas_all_path:, compile:, output_directory: "_s
           Utils.log "Compiling complete collection..."
 
           # TODO: Why will defining a collection immediately compile??
-          metanorma_collection = Metanorma::Collection.parse(collection_config_path)
+          metanorma_collection = Metanorma::Collection.parse(new_collection_config_path)
 
           # TODO: Somehow this is no longer used
           collection_opts = {
diff --git a/lib/suma/schema_collection.rb b/lib/suma/schema_collection.rb
index 200c401..99dbadc 100644
--- a/lib/suma/schema_collection.rb
+++ b/lib/suma/schema_collection.rb
@@ -78,6 +78,8 @@ def compile
         entry.save_exp
       end
 
+      # DISABLING FOLLOWING CODE AS MISCONCEIVED. THE SCHEMA DOCUMENTS
+      # BELONG IN THE MAIN COLLECTION NOT HERE
       docs.each_pair do |schema_id, entry|
         entry.compile
       end