This post will explain creating custom Core ships for your Scenarios or Personal Use.

Designing how the ship looks:
First thing you'll need to do is... create a ship! Here you will design how your core ship will look. Until an out of game editor is available, it's easier to use the in-game shipbuilder rather than text editing (unless you know all the hardpoint names/locations and component names by heart). The core ships i've created have always been available to every race, but i'm not sure if this is a bug or not. To be safe, I recommend designing what the core ship looks like for all 5 ship styles (well 6 including Dread Lord but I can't seem get DL hulls to show in ship builder). The design does not need to look like what the ship will actually have, or even the same hull size (though this could mislead users about what size the ship is). If you want a ship to look like it has way more than it actually does then you could use 0 size components during the designing (it will be easy to do this when the mod folder works by having a mod for your designing with 0 size components). As of posting, you can name the related designs the same name to easily remember which is which, because it doesn't replace the file we are going to be using.
Example: Created terran style small ship (small hull 0) with some jewelry, added a laser0 (from laser technology, not space militarization), and saved it with the name Blaster. Created drengin style small ship with different jewelry, added a laser0, and also named it Blaster. Same for all the other styles.
Now that you've made some cool looking ships, named, and saved the designs lets get them in the right spot.

Moving your designs for core ship:
In MyDocuments\MyGames\GalCiv2\Ships you will find your list of designs you created. The files you are looking for start with S0_-S5_ (the number is the style) and have the extension shipcfg. Copy these (only the ones you designed to be core ships, not every single shipcfg) into (main game folder until mod folders...)\Data\ShipCfg. Now you need to rename those files. This is the name you will be using to uniquely identify each group of core ships, so it needs to be the same as all it's related designs but different from any other design. Do not remove the style (S0_-S5_) from the filename, but you can take out the UD_ if you want (stands for User Design). If you used the same name, then you most likely just need to remove the number at the end of the shipname.
Example: moved S0_UD_Blaster0.shipcfg and renamed it to S0_Blaster.shipcfg. moved S3_UD_Blaster1.shipcfg and renamed it S3_Blaster.shipcfg. Same for other styles.
Now we can add the ships to the game.

Editing GC2ships.xml:
Open (main game folder until mod folders...)\Data\English\GC2ships.xml with whatever editor you use (I prefer using VC++ since I use it for c++). Find a spot between [/DataChecksum] and [/GC2Ships], but not inside another ship. The first tag is Ship and assigns a string to Name. The name in quotes is used by the game and needs to be unique. Next is DisplayName, which is what you will actually see the ship called in game. Model needs to be the filename of the design without the style (S0_) or the extension (.shipcfg). This is only what the ship looks like and has no effect on gameplay. After that you can add a description for the ship that shows up ingame. I'll cover components in the next section.
Example:
[Ship Name="MyBlaster"]
[DisplayName]Big Bad Killer[/DisplayName]
[Model]Blaster[/Model]
[Description]This is an example core ship[/Description]

Adding Components:
Before adding components there are a few things you need to remember. The components you add do not need to be like your design. You could have your design look like a cargo hull with 10 lasers and 3 engines, but the actually ship only have 1 laser and no engines on a small hull. The opposite is the same too as you could have your design look like it only has 1 laser, yet actually have 3. This leads me to another detail, don't try to overfill the size. The game knows how much space the components take, so adding 100 laser components in the xml will lead you to never having the core design available. The design becomes available once all the tech requirements for the components are met as well as the size requirement. Miniaturization is considered when determining the size. For this reason, unless you know what you're doing, it's best to keep the components added, the same as the design. If you can't remember what components you put on (or know their coded name) they can be looked up very easily. All you have to do to see what is on your design is open the shipcfg in a text editor. There will be a BASE_HULL that has the name of the hull you used (with the style at the front and a .x at the end) as well as either DUMMY## or P## each with the component names (again with the style and .x). Add the components starting with the hull (don't enter in the style or .x) and then the other components you actually want on the ship. Close it off with [/ship] and save. You only need to add one ship enter per group of related designs (matching styles).
Example:
[Component]SmallHull0[/Component]
[Component]Laser0[/Component]
[Component]HyperDrive[/Component]
[/Ship]
Note that the HyperDrive was not part of the design. This core ship will become available when the player has researched HyperDrives and LasersAnd now you have a user created core ship design! One more thing you need to know about core ships. You can not upgrade them in the ship builder (or delete them, just obsolete). While it's a shame that you can't redesign them with better techs on the fly ingame, it' has to be this way because there's no way to differentiate between what is jewelry and what is not. You can still upgrade built core ships to designs you make ingame that match in hull size like normal.

For those who might want it is a small table of ship styles:
S0 - Terran Ship Style
S1 - Torian Ship Style
S2 - Yor Ship Style
S3 - Drengin Ship Style
S4 - Altarian Ship Style
S5 - Dread Lord Ship Style

Please post any errors I may have made, or bugs you come across with user created core ships.
Feel free to reorganize this data and add it to the wiki! While a little credit for it may be nice (originally by Syneris, fixed edited updated etc by...), it's not necessary as long as it gets added on the wiki to help people who may want it.