The Skills are in starfarer.api\com\fs\starfarer\api\impl\campaign\skills. To implement new ones, you'll need to create a directory (preferably in /scripts) and move one of the Skill java files there, change the reference in the .skill file, etc.
Thanks for the help! With a little digging and playing around I was able to get started on my some of my ideas. My first test was to try and combine 'Strike Commander' in to 'Missile Specialization', and then remove the 'Strike Commander' skill from the game. I am running in to 2 complications I was wondering if you or someone else might know how this is supposed to be done.
Firstly, It appears that the game is still reading the base-game skill info for 'Missile Specialization' and inputting the stats with my modified version (as seen in the attachment). As you can see for my test the only value I changed was 'Level 3: Missile damage' from 25% to 10%. However it is still reading the 25% from the base-game value and dumping it in extra with my modified stats.
Secondly, I can tell if I remove the 'Strike Commander' skill entry from skill_data.csv in the default sub-directory (starsector-core/data/character/skills) that it will no longer appear on the character screen as a learn-able skill. However I'm not sure how to remove this from showing from a mod standpoint. If I copy the skill_data.csv to my mod folder/data/character/skills and remove the 'Strike Commander' entry it appears to have no effect. I'm also not sure if this will prevent the AI / Officers from being able to learn this ability.
Edit: Also wanted to throw in that I tested this with harpoon MRM pod - 4x 750 damage harpoons hit a hammerhead shield for 1620 damage, which is equivalent to 2025 damage after dividing by .8 for the shield mitigation. Since harpoons deal 1/2 damage to shields, 4x 375 = 1500 * 1.35 (25 % + 10%) = 2025 so I confirmed that both the mod values and the standard values are being added.
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