Added a clone analysis script.

Will clone analyses in the db and config files. By default the script expects a pipeline style db. It will clone from one analysis (already present in the db) to a set of new logic names specified in the input file. By default it will clone the entry in the analysis table, the input id type and any rules of the original analysis. A set of config files can be specified on the second line of the input file. If present the analysis entry in these configs will be cloned to the new logic names in the input file. Configs that are being cloned will be backed up by the script, however it is recommended that you back them up if you haven't checked them into git.

Optional flags include: -no_rules (don't clone rules), -not_pipeline_db (don't clone rules or input id type), -just_config (don't touch the db tables and only clone in configs). Consult the help to see all options.

Care should be taken when cloning analyses, especially for rules and paths to output dirs in BatchQueue.pm. For BatchQueue.pm output paths, remove the output path (if present) from the analysis being cloned and make sure the default path is set. Cloned analyses will then use the default output dir path with their logic name appended onto them.
updated deprecated call
* added --sourcepass option to allow use of password-protected
  source mysql instances