For the original Entrenchment, Diplomacy expansions, and now Rebellion, you only have to include the files that you want to change and if you want to "remove" an original file you have to remove it from the entity manifest (which is explained in the documentation). Also note that it includes some reference files which are outdated and you will need to create your own or download the 7-z archives for Rebellion that includes all current versions.
Each faction can build a max of 9 tactical structures, 9 logistical structures, 1 titan class, 9 capital class, 9 frigate class,and 9 cruiser class, (note that frigates and cruisers are the same, but they are just shown on different places in the U.I.). You can also place tactical modules in a logistics slot and vice-versa. An entity can have a max of 5 different weapons. As far as it is known there isn't any limit on research levels.
The first thing on a new modder's list should be the Developer.exe's. Weather you are starting to build a new mod or testing a downloaded mod this tool is very useful for finding errors and game testing. If you are not sure about the errors generated or you want to keep track of them you will want to enable logging, then you can copy the information to paste into a thread in the modding forum.
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