Script out Oracle DDL in an automated fashion
The reason you are having problems with dbms_metadata.get_ddl is that it outputs CLOBs which can be up to 4GB in size.  By default, SQL*Plus and Oracle SQL Developer truncate long text so they don't trash the client with large gobs of text.  

It's very easy to override this behavior in SQL*Plus with a few SET commands and get clean DDL.

The script you need is:

-- Run this script in SQL*Plus.

-- don't print headers or other crap
set heading off;
set echo off;
set pagesize 0;      

-- don't truncate the line output
-- trim the extra space from linesize when spooling
set long 99999;      
set linesize 32767;  
set trimspool on;    

-- don't truncate this specific column's output
col object_ddl format A32000;

spool sys_ddl.sql;

SELECT dbms_metadata.get_ddl(object_type, object_name, owner) || ';' AS object_ddl
FROM DBA_OBJECTS
WHERE 
      OWNER = 'SYS'
  AND OBJECT_TYPE IN (
      'TABLE'
    , 'INDEX'
    , 'SEQUENCE'
    , 'VIEW'
  )
ORDER BY
    OWNER
  , OBJECT_TYPE
  , OBJECT_NAME
;

spool off;