I have done worse mistakes!

Yep, it's hardcoded. But you can replace existing abilities by your own:)

If XMLSchema was not hardcoded, than I could have actually pulled it off. With exception of that it worked perfectly.

Actually, you can get around things by adding levels to abilities. For example, I added a level '5' to the Berserk spawn that summons 6 Elite berserk fighters, and made a new special ability for it. This allows me to add different summons without affecting the other character's abilities.

do I need to start new game if I make changes? I tried to change Mastiff's HP but doesn't work. Also how can I add missiles to the motherships? an erlier post by Nanaki says something about models. Where are they located?

If you want to see changes on Mastiff (or any other ship) you need to find save before you get it. In this case find save with pirate version mastiff and go to the Elio for aerogrphy quest.
I never tried missile lunchers on mothership so I don't know if they work.
Model files are here ..\Data\OBJECT\*.imd. You need a IMDeditor to change things.

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I have another problem:

Now buying code looks like below and works ok

but you can buy only one mothership. If you try to buy second you get CTD. It is caused by group declaration "myGroup_1". Separate group must be attached to each mothership so I changed code slightly (added 3rd column to table) and now looks like this:

but unfortunately it doesn't work. No errors and no visible effects. Maybe someone could check the code and find out what's wrong?

I am not sure myself, but, I do not see where ship_nm_1 is defined... You are probably better at this than I am, though, so I could be completely clueless.

In other news, I have successfully implimented summoning fleets to the specials.script. With my test script 'MSF Summon 4', you can summon 1 squadron of fighters, 1 squadron of bombers, and 1 Stalingrad-class Battleship.

where can we change the perks properties like accuracy and stuff?

Changing what a perk is done is dependant on the perk itself. Most of the pilot/gunnery/system perk attributes can be found in the data/script/ai/perkdispatcher.script file...

In other news, I have squeezed out all the knowlege I can out of the specials.script, now I am currently working on all Location scripts.

My first mod project is to double the amount of random spawns in all sectors. This is a simple affair, mostly just time-consuming.

My second mod project is to introduce actual civil war, Old Empire and New Empire elements fighting in various sectors (odd how there is no fighting for what is supposedly a 'war'). So far, my plan is that all Old Emipre sectors that get taken over by the New Empire later in the game will have New Empire ships spawning in them. My plan is to also have some boarder New Empire sectors get the occasional Old Empire incursion as well. May also adjust the random spawns on a per-system basis, such as introducing Patrol spawns to Kruger (Kruger is currently a loot bonanza because nothing but traders spawn, in a system crawling with pirates.)

My third mod project after that is... I have not decided yet.

wheres the Alien_Dreadnought_0's ini? I want to make the dreadnought my mothership but can't seem to find the .ini in the TEXTURE\Interface\Carcass\Slots folder. Is it somewhere else? I will try and just add components to shipdescription.xml in the meantime if no .ini exists. Also how are the .ini connected to the ship? How does the game decide which one to use? Also when I change ship HP and shields it doesn't show when I load a saved game but when I change the mesh it shows in game. Is there a way to make them work? If not where are the scripts that give the various motherships? I could change the scripts to give me the same ship throughout the game.

Well, I accomplished both my Modding goals, and so far the results have been good. Systems are a LOT more active, I also added NESF incursions in seven MSF systems, and NESF ships spawn regularly and engage with MSF patrols. Overall, it works beautifully.

Ships that are not meant to be controlled by the player, such as the Stone Arrow, Alien Dreadnought, and Stalingrad Battleship will have no INI and their IMD file will be missing a lot of needed data. I highly recommend not using these ships unless you are well versed in creating INIs and modding IMD files.

You know when you click on a ship while docked, where it shows all the ship components and allows you to add/remove components? Thats what the INI handles.

I suggest you load a save before you acquire a certain mothership. Once a ship is spawned, its stats are static. The only way you can change it is by loading a save before that ship spawns.

They are quest scripts (look in the quest folder). Goblin Wizard was working on a script that could allow you to purchase whatever motherships you want, but im not sure if that went anywhere actually.