As far as I know, I haven't deleted them, but I was looking thru the debug file, just to see what it looked like, and it looks as if as I was starting the game, it tried ot find pirate and strbase configurations for all the races and it couldn't find them. Is it because you don't start with any of those? I just want ot make sure I didn't mess anything up. Any help is appreciated. I've copied the listings below:

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Debug Message: Could not find ship config: S2_PirateShip.shipcfg. This core ship will not be available for style Altarian Resistance Style.
Debug Message: Could not find ship config: S3_PirateShip.shipcfg. This core ship will not be available for style Arcean Empire Style.
Debug Message: Could not find ship config: S6_PirateShip.shipcfg. This core ship will not be available for style Dominion of Korx Style.
Debug Message: Could not find ship config: S7_PirateShip.shipcfg. This core ship will not be available for style Drath Legion Style.
Debug Message: Could not find ship config: S13_PirateShip.shipcfg. This core ship will not be available for style Dread Lords Style.
Debug Message: Could not find ship config: S1_PirateShip.shipcfg. This core ship will not be available for style Drengin Empire Style.
Debug Message: Could not find ship config: S9_PirateShip.shipcfg. This core ship will not be available for style Iconian Refuge Style.
Debug Message: Could not find ship config: S10_PirateShip.shipcfg. This core ship will not be available for style Korath Clan Style.
Debug Message: Could not find ship config: S11_PirateShip.shipcfg. This core ship will not be available for style Krynn Consulate Style.
Debug Message: Could not find ship config: Pirate_PirateShip.shipcfg. This core ship will not be available for style Pirate Style.
Debug Message: Could not find ship config: S0_PirateShip.shipcfg. This core ship will not be available for style Terran Alliance Style.
Debug Message: Could not find ship config: S8_PirateShip.shipcfg. This core ship will not be available for style Thalan Empire Style.
Debug Message: Could not find ship config: S4_PirateShip.shipcfg. This core ship will not be available for style Torian Confederation Style.
Debug Message: Could not find ship config: S5_PirateShip.shipcfg. This core ship will not be available for style Yor Collective Style.
Debug Message: Could not find ship config: S2_Starbase.shipcfg. This core ship will not be available for style Altarian Resistance Style.
Debug Message: Could not find ship config: S3_Starbase.shipcfg. This core ship will not be available for style Arcean Empire Style.
Debug Message: Could not find ship config: S6_Starbase.shipcfg. This core ship will not be available for style Dominion of Korx Style.
Debug Message: Could not find ship config: S7_Starbase.shipcfg. This core ship will not be available for style Drath Legion Style.
Debug Message: Could not find ship config: S13_Starbase.shipcfg. This core ship will not be available for style Dread Lords Style.
Debug Message: Could not find ship config: S1_Starbase.shipcfg. This core ship will not be available for style Drengin Empire Style.
Debug Message: Could not find ship config: S9_Starbase.shipcfg. This core ship will not be available for style Iconian Refuge Style.
Debug Message: Could not find ship config: S10_Starbase.shipcfg. This core ship will not be available for style Korath Clan Style.
Debug Message: Could not find ship config: S11_Starbase.shipcfg. This core ship will not be available for style Krynn Consulate Style.
Debug Message: Could not find ship config: Pirate_Starbase.shipcfg. This core ship will not be available for style Pirate Style.
Debug Message: Could not find ship config: S0_Starbase.shipcfg. This core ship will not be available for style Terran Alliance Style.
Debug Message: Could not find ship config: S8_Starbase.shipcfg. This core ship will not be available for style Thalan Empire Style.
Debug Message: Could not find ship config: S4_Starbase.shipcfg. This core ship will not be available for style Torian Confederation Style.
Debug Message: Could not find ship config: S5_Starbase.shipcfg. This core ship will not be available for style Yor Collective Style.