It seems there is a missing db_initial_setup call in the local file branch. Can't currently test if the patch below works (no access to my development machine)

<verbatim>
--- src\clone.c
+++ src\clone.c
@@ -60,10 +60,11 @@
   if( g.urlIsFile ){
     file_copy(g.urlName, g.argv[3]);
     db_close(1);
     db_open_repository(g.argv[3]);
     db_record_repository_filename(g.argv[3]);
+    db_initial_setup(0, zDefaultUser, 0);
     db_multi_exec(
       "REPLACE INTO config(name,value)"
       " VALUES('server-code', lower(hex(randomblob(20))));"
       "REPLACE INTO config(name,value)"
       " VALUES('last-sync-url', '%q');",
</verbatim>