[sonicintuition]

There is a post directly above yours that states what commands.pl is. Read it.

Regarding the errors with NPC's:

Source this into your database:

ALTER TABLE spawnentry ADD spawn_limit TINYINT NOT NULL DEFAULT '0';
ALTER TABLE npc_types ADD spawn_limit TINYINT NOT NULL DEFAULT '0';
ALTER TABLE character_ ADD extprofile BLOB NOT NULL;
ALTER TABLE npc_types ADD npc_aggro TINYINT NOT NULL DEFAULT '0';
ALTER TABLE npc_types ADD attack_speed FLOAT NOT NULL DEFAULT '0';
ALTER TABLE npc_types ADD findable TINYINT NOT NULL DEFAULT '0';
ALTER TABLE spawn2 ADD condition MEDIUMINT UNSIGNED NOT NULL DEFAULT '0';
ALTER TABLE spawn2 ADD cond_value MEDIUMINT NOT NULL DEFAULT '1';

That should alleviate the problem you are having.

Regards,
SI