Metacat

Replace System.out.println statements with logMetacat statements.

Update replication documentation and fix code so that replication log is available.

Separate the concept of a backup file location and a metacat external directory location. These can be totally different.

Fixes include:
-Overwriting existing DTDs on the filesystem if they exist and registration in the DB failed
-only registering a DTD once

do not include the column name when inserting into an auto-increment column

Make sure and write the shortcut to the backup directory to a directory in the users home.

Allow for backup properties to be written to context based subdirectory of the external configuration directory. This allow multiple instances of metacat to be run side by side.

Change name of writeTempFile to writeTempUploadFile since this instance deals with the temporary upload dir specifically

Added exception to error xml to clarify error to api.

writeTempFile was trying to write the same file as the registry. Changed to write the file to an "upload" subdirectory. Also throws IOException so errors get reported back to api.