Kaphotics

pk3DS works on unpacked ROM data, which can be dumped from a cart or installed data. You can rebuild the ROM however you want (with other tools) when you are done editing the files. UPR does not work on 3DS games, thus it does not have anything to do with CIA files.

Has been fixed since the last release, please wait for the next update

PKHeX detects RB vs Y by checking the event var for "Starter Received", since there isn't really much else different between versions. If you received nothing, it's RBY, if you received Pikachu, Y, and otherwise RB. I can probably change the logic a bit to force Yellow/etc

The blank save file type is indicated at the top. If it's "RBY", it uses the Red/Blue personal data.

Fixed damage moves are fixed damage in the game code; the game overrides the calculated value based on the move ID. This isn't something pk3DS is set up to modify (too complex).

Undocumented, thus not implemented.

The program is preventing you from saving a totally illegal 'mon with normal program operation. The training wheels are in place to prevent unintended consequences; working as intended.

done: Update blank sav3 behavior: https://github.com/kwsch/PKHeX/commit/53b2ca93b8fb4685d51c0392a0ce70a7bf8c0516 Merge game selection alert & prompt to 1 popup https://github.com/kwsch/PKHeX/commit/9fd6d86b1dfbbcaa9c7cbe2c1ff623457c079eb4

Script engine is the same as gen6 and gen7; however, the scripting engine reverse engineering has never been fully unlocked like prior games. I can't do everything Without script editing (and overworld editing), no addition of interactable content.

Sure, hack the ROM so it doesn't heal, or change the base stats for a similar effect. Unrelated to PKHeX.

No, it just copies your team to another location and refreshes their stats. They'd want to remove any temporary status effects or dips in HP prior to starting.

Hitting "Save" is required for the program to know it needs to write the final data. If you don't want to save your changes, you press X instead.

Physical/digital doesn't matter; you just need an exploitable console (RCM exploit isn't patched). If you got the console before last May you'll be fine, otherwise, you're probably out of luck.

Dump: It copies it to your clipboard and plays a sound indicating it did something. It works like the other dump buttons. Trainer Pokemon: you have to set them back after editing each one IV/EV buttons: Maybe i'll add it if I get around to doing more quality of life updates/fixes

Read the error message; you have to install something else.