bugfix: reset the tried jobs to retry_count=1 and untried ones to retry_count=0 when doing a bulk reset

methods dbconn_2_mysql(), dbconn_2_pgsql(), db_connect_command(), db_execute_command() are DEPRECATED - use db_cmd.pl instead

added support for -pipeline_url as an input parameter (no need to supply hive_driver or password in this case)

now performing deep-stack substitution for whatever is dataflown into tables (rather than just dataflowing the output_id)

bugfix: substituting the accu signature on demand from the very depths of emitting job's param_stack

bugfix: make sure longer input_id hashes are correctly fetched from analysis_data table in "param stack" mode

Simplified interface: now db_cmd.pl understands 'CREATE DATABASE' and 'DROP DATABASE' without parameters, given a full URL.

Can now do a mysqldump given a URL or Registry data, using a newly supported -to_params option. Note the necessity of 'eval' before 'mysqldump' (it removes quotes around the password).

Updated schema diagram and description file that include param_id_stack and accu_id_stack in job table.

"parameter stack" implementation using two extra fields in job table. Accu content intended for any job_id has preference over Input_id content for the same job.

Dataflowing minimal information out of Runnables, relying on templates in PipeConfig file to extend it if needed

Bugfixes to pacify pgsql: changed a non-functional "HAVING" into a nested SELECT, and changed unsupported SUM() into COUNT(CASE … )

An important comment about UNIX sockets (without a port number) vs TCPIP sockets (with a port number).

Expose parts of pipeline_db, make them less EnsEMBL-specific, allow multiple failover initializers and use self-reference if none of them worked. Phasing out $self->o('ENV', …) expressions

Allow skipping the port number; you no longer need to define your port if you are happy with driver's default (thanks to db_conn.pl and core's DBConnection)

Registry support is now cenralised in DBAdaptor, so scripts just pass reg_* options into the constructor. Passing -reg_type allows to connect to originally non-Hive Registry entries.

Start using the new db_conn.pl script instead of building driver-specific commands and running them.