So, did this mean the Photo Club was originally intended to be in SM, a similar feature that was planned for SM (which the one in USUM could probably have been intended to be an upgraded version of), or was it believed to be something different (like actually being able to put clothing on certain Pokemon)?
Pretty much this. I only mentioned the photo club because of the similarities, but I don't think they were related since one was 3D models and one was 2D stamps. The photo club is more like the accessories from Gen 4 to be honest.From what he describes in the code it sounds like you were going to be able to put stuff, like ribbons and such, on the actual Pokemon model. It wouldn't surprise me if there was a photo mode attached to it, so they might've dusted off that code and turned it into the photo club in USUM, but the original purpose sounds different.
It wouldn't surprise me if there's similar strings for Let's Go's ability to decorate the parnter Pikachu & Eevee, though.
Also GOOD point about Let's Go. I didn't remember that feature but that's a perfect comparison and maybe the same feature fully realized.
It's hard to say, game mechanic-wise it may have been "badges" but they may have already had the stamp concept planned out for whatever time before it was implemented. Either way the badge code was left over from the previous games, so I would guess probably more the latter. There are a couple commits relating to the trainer pass and stamps (スタンプ) before that (November 10 2015/2f8ce7949545) and the obedience system had to be changed from being based on badge count to specific values per stamp.So, did this mean the rewards were at one point still intended to be Badges but later changed to the Stamps? Or did they just keep the value name as "badge" until they got far enough in development to have an official name of the Badge's replacement?
The box judge flag was added on Aug 16 2015. (d1e8bd1d)
Ball throwing style and days since last Refresh save data was added on Dec 5 2015. (da5b2ee42)
Trainer ball type support was added on May 26 2015. (9dd18115)
This is part of code for determining what mega item trainer types use. This listing was added on Jan 19 2016. (40bbd04dd) For some reason the comments here mention Sina/Dexio being gym leaders. The other battle tree NPCs have mentions here too. For some reason Cynthia is called a BW npc and Anabel is labeled under RS, while Colress gets the more specific BW2.TrainerTypeData.cpp said://メガリング
case TRTYPE_GINA: //ジーナ（XY登場NPC）但しデータ上で持たない可能性もある。
case TRTYPE_GINA2: //ジーナ（XY登場NPC）ジムリーダー就任後
case TRTYPE_DEKUSIO: //デクシオ（XY登場NPC）但しデータ上で持たない可能性もある。
case TRTYPE_DEKUSIO2: //デクシオ（XY登場NPC）ジムリーダー就任後
The only other mention of Sina is a commit from Aug 25 2015 (987882bc489) adding code to check if a 10% Zygarde is the one that she presumably would give you. There's a mention of pokedeco in the params but not much else. The code was later removed in Jan 28 2016 (06ab303fb8). In final SM you only get a Zygarde cube from them, but USUM does have a 10% Zygarde gift though it's not really that special to warrant any checking.
The Zygarde cube functionality would be added on Nov 30 2015 (47df53e4cad).[modify]ジーナのジガルデ10%を判定する関数追加。中身がまだ不十分
Originally the Zygarde cube could teach Crunch and Outrage, but this was changed on Jan 14 2016 (3cea7dfb6) probably because it already learned those by level up. Zygarde cell scripts would be added on Jan 17 2016 (7c425020e4664) and Zygarde core functionality on Jan 21 2016 (2d0d42056b5c).
Some final items named "???" are actually mentioned by name in itemsym.h, though only a testing copy that lacks mid-development history. Refer to https://bulbapedia.bulbagarden.net/wiki/List_of_items_by_index_number_(Generation_VII) for index numbers.
ITEM_PURIANOHANA ( 837 ) // プリアのはな
ITEM_BISUKASUNOHANA ( 838 ) // ビスカスのはな
ITEM_BATOBARADANOHANA ( 839 ) // バトバラダのはな
ITEM_KURAUNNOHANA ( 840 ) // クラウンのはな
Apparently these are all flowers, right after the z-crystals. I don't know what these mean (using machine translation) but I would guess they would have to do with the 4 islands.
#848 after the Zygarde cube is a different "complete cube". Its use was removed on Feb 17 2016 (fa4161686a), having the same use check as the regular Zygarde cube.
ITEM_KANZENKYUUBU ( 848 ) // かんぜんキューブ
"Kukui's letter" apparently.
ITEM_KUKUINOTEGAMI ( 859 ) // ククイのてがみ
The rest are just named dummy items.
861-878 = event dummy 3-20 (イベントダミー)
885-898 = normal dummy 7-20 (ノーマルダミー)
899-903 = "recovery" dummy 1-5 (かいふくダミー)
EDIT: There was a bugfix/change to the Zygarde cube on May 11 2016 (a7a94727387e).
You used to need the Zygarde Cube in the bag to activate Power Construct in battle, but apparently a game without the cube fighting a game with the cube would check their own bags and desync/end the battle when trying to transform.