These changes have been made since the current 2.2.0 release. If you build the project as-is, it will include all of them.
What's the point of going through all the trouble of the debug process if you're going to go and fiddle with the game afterwards…?
— Satoru Iwata, "Iwata Asks – Pokémon HeartGold Version & SoulSilver Version"
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Add: Medicine and Berry pockets in the Bag.
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Add: Store up to 30 phone numbers in Pokégear.
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Add: Always keep the option to Teleport away from Indigo Plateau.
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Add: Portrait for the meteorite in Pewter Museum.
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Add: Special sprite for Red's Pikachu.
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Add: Johto and Kanto forms for Arbok.
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Add: Drain Kiss drains 75% HP.
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Add: Update Pokémon, move, and item attributes to Gen VII:
- Super Potion heals 60 HP.
- Hyper Potion heals 120 HP and costs ¥1500.
- Fresh Water heals 30 HP.
- Soda Pop heals 50 HP.
- Lemonade heals 70 HP and costs ¥400.
- X items sharply raise stats and cost twice as much.
- Tackle has 40 power.
- Sucker Punch has 70 power.
- Leech Life has 80 power and 10 PP.
- Thunder Wave has 90% accuracy.
- Swagger has 85% accuracy.
- Paralysis halves (not quarters) Speed.
- Burn does 1/16 (not 1/8) damage per turn.
- Confusion has a 33% chance (not 50%) to hit self.
- Gengar has the ability Cursed Body. (Can also have Levitate in non-Faithful.)
- Raikou, Entei, and Suicune have the hidden ability Inner Focus. (Faithful only.)
- New item: Protect Pads (abbreviated "Protective Pads"). "Protect the holder from effects caused by making direct contact with the target."
- Timer Ball catch rate multiplier is 1 + (turns passed × 3) / 10.
- Nest Ball catch rate multiplier is (41 − enemy mon level) / 5.
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Add: Flash is required to return Falkner to the Gym.
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Add: Replace Spike Cannon with Icicle Spear.
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Add: Replace Twineedle with U-turn.
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Add: Replace Whirlwind with Sucker Punch.
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Add: Replace Vital Throw with Aura Sphere.
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Add: Replace Nightmare with Facade.
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Add: Replace Submission with Close Combat.
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Add: Replace Sand-Attack with Toxic Spikes.
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Add: Replace Fairy Wind with Bulldoze.
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Add: Replace Metal Sound with Roost.
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Add: Replace Sky Attack with Brave Bird.
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Add: Replace Twister with Aqua Jet.
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Add: Replace Sludge with Venoshock.
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Add: Replace Egg Bomb with Skill Swap.
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Add: Replace Mist with Amnesia.
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Add: Replace Fury Cutter with Bug Bite.
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Add: Replace Harden with Rock Blast.
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Add: Replace Triple Kick with Drain Punch.
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Add: Replace Lock-On with Power Whip.
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Add: Replace Flail with Gyro Ball.
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Add: Replace Flame Wheel with Flame Charge.
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Add: Replace Moonlight and Morning Sun with Knock Off and "HealingLight".
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Add: Replace Fury Attack and Fury Cutter with Trick and "Fury Strikes".
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Add: Giga Impact.
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Add: NPC trainers can have nicknamed Pokémon.
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Add: NPC trainers can have custom EVs.
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Add: Accuracy and evasion work like in Gen VI.
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Add: Substitute blocks sound-based moves.
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Add: Gen III critical hit mechanics (ignore -Atk and +Def stat changes, don't ignore burn).
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Add: Grass-type Pokémon are immune to PoisonPowder, Stun Spore, Sleep Powder, and Spore.
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Add: Marowak is Ground/Ghost.
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Add: Charizard is Fire/Dragon.
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Add: Yanmega is Bug/Dragon.
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Add: Ampharos is Electric/Dragon.
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Add: Noctowl is Ghost/Flying.
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Add: Bellossom is Grass/Fairy.
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Add: Celebi is Grass/Fairy.
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Add: Rapidash is Fire/Fairy.
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Add: Octillery is Water/Fire.
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Add: Politoed can learn Energy Ball.
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Add: Pidgeot can learn Focus Blast.
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Add: Misdreavus can learn Disarm Voice.
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Add: Espeon can learn Power Gem.
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Add: Dig has 90 BP.
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Add: Give in-game trades good natures.
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Add: TM prices from OR/AS.
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Add: Show quantity in Bag in marts.
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Add: Fancier Bag interface with color-coded pockets.
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Add: Get a free Premier Ball with every 10 Balls bought.
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Add: Show Pokémon portraits when using field moves (thanks to TPP:AC).
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Add: Time boundaries from HG/SS (day lasts until 8 PM, not 6 PM).
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Add: Use DVs to vary Pokémon colors like in Stadium.
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Add: Update random Wonder Trade OT names.
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Add: Teleport switches in trainer battles, like Let's Go.
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Add: Rock Smash has 60 power (non-Faithful).
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Add: Strength is Fighting-type (non-Faithful).
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Add: Submission has 120 power (non-Faithful).
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Add: Trainers have max happiness for Return.
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Add: 1/2048 chance for Wonder Traded Pokémon to have Pokérus.
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Add: Buy 12 Moomoo Milk at once.
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Add: Show TM names before buying them and when picking them up.
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Add: Say which pocket is full if an item can't be picked up.
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Add: Use Yellow's encounter music for Jessie & James.
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Add: Large red Gyarados sprite.
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Add: Route 23 between Pokémon League Gate and Victory Road.
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Add: Oak's lab looks different from Elm's lab.
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Add: Grass-green for Faraway Island.
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Add: TM prices from OR/AS.
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Add: Update random Wonder Trade OT names.
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Add: Respawn roaming beasts when released.
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Add: Mr. Pokémon gives you a non-OT Ditto, not an Egg, for the Masuda breeding method.
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Add: Use original Jynx sprite.
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Add: Make overworld sprites darker at night.
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Add: Goldenrod Dept. Store and Celadon Mansion roofs have a dark sky at night.
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Add: Olivine Gym has its two trainers from HGSS.
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Add: Unlock frame type 9.
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Add: Choose a typeface/font.
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Add: XY Bicycle music for Cycling Road.
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Add: Prof.Oak gives you the Oval Charm for seeing all 254 Pokémon, and the Shiny Charm for catching all 254.
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Add: Prof.Elm is in the intro.
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Add: Cosplayer, Bug Maniac, Ruin Maniac, Lady, Baker, Tamer, Artist, Aroma Lady, Sightseer♂, and Sightseer♀ trainer classes.
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Add: New Trainer Card based on the Name Cards from the Mobile Adapter system.
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Add: Show PC box quantity.
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Add: Pokémon stats show caught Poké Ball.
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Add: Nest, Net, Dive, Luxury, and Heal Balls.
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Add: Cerulean Bike Shop from HGSS.
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Add: Elite 4 rooms have floor arenas.
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Add: Confirm gender selection.
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Add: Colored party Pokémon icons.
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Add: Magikarp Jump patterns.
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Add: Headbutt trees to get Silver and Gold Leaves.
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Add: Smash rocks to get various items.
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Add: Item maniacs from B/W.
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Add: Fish to get items based on the Rod (Bottle Caps with Super Rod).
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Add: Mulch regrows Berries.
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Add: Three battle styles: set, switch, and predict.
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Add: Battle Scene → Battle Effects.
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Add: Final Lyra battle.
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Add: Use a Ball on an already-caught Pokémon to change its Ball.
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Add: Kurt makes Balls right away.
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Add: Bug-Catching Contest prizes from HGSS.
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Add: Hidden Grottoes.
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Add: Unown ! and ?.
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Add: In-battle symbol to show that Nuzlocke mode prevents capture.
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Add: More Grass-type Pokémon can learn Earth Power and Earthquake.
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Add: Status icons in battle.
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Add: You can Wonder Trade Eggs.
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Add: Hidden Power guru finds your Pokémon's Hidden Power.
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Add: Hidden Power can be Fairy-type in non-Faithful.
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Add: Reset initial options by pressing Left+B at the title screen.
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Add: Music resumes where it left off after a battle (from TPP).
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Add: Use a proper menu for resurrecting Fossils.
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Add: Press B in the battle menu to move the cursor to Run.
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Add: Music player with piano roll by Sanqui.
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Add: Instant text option.
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Add: Imperial or metric units.
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Add: 12-hour or 24-hour clock.
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Add: ABC or QWERTY keyboard.
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Add: Item icons in the Bag.
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Add: Thrown Balls use individual icons.
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Add: Pokédex shows shiny palettes after getting the Shiny Charm.
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Add: New Game+ preserves your money, Battle Points, and PC Pokémon.
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Add: Phone call trainers ask automatically for your number.
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Add: Replace Jigglypuff Poster with Marill Poster.
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Add: Briefly beep to warn of low HP.
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Add: Play B/W final Pokémon music for Gym Leaders and Elite 4.
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Add: New title music after beating the Elite 4.
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Add: Larger Kanto routes, like in RBY.
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Add: Proper inverted colors in battle (by MeroMero).
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Add: Evolution moves from Gen VII.
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Add: Move Reminder supports pre-evolution and evolution moves.
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Add: Dark battle intro at night.
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Add: Evening as a time of day (shares wild Pokémon with night).
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Add: Trainer battles can be forfeited.
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Add: Show genders in party menu.
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Add: Show weather icons during battle like Gen 5+.
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Add: Vending machines have a 1/32 chance of giving an extra item.
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Add: Cross whirlpools, don't remove them (like HGSS).
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Add: Rename RageCandyBar to Cake of Rage.
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Add: Rename Guard Spec. to Guard Stats.
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Add: Rename Kay to Carrie (from Pokémon Stadium 2).
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Add: Rename Slowbro to the Squatter Pokémon. https://lparchive.org/Pokemon-Blue/code.html
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Fix: Lt. Surge's electric fence color does not override speech bubbles.
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Fix: Zap Cannon has 120 power.
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Fix: Pay Day pays 5 times the user's level, not 2.
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Fix: Explosion and Self-Destruct do not halve Defense.
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Fix: Quick Ball catch rate multiplier is 5 on the first turn.
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Fix: Minimize raises evasion by two stages.
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Fix: Gen 7 critical hit chances (1/24, 1/8, 1/2, 1/1)
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Fix: Munchlax, Magnezone, and Tangrowth have their relatives' cries.
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Fix: Game console names in room.
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Fix: Yellow Forest gate clerk does not face you.
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Fix: Read hidden Ruins of Alph tablet from one direction.
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Fix: Ice Rock tile collision data.
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Fix: Adjust some trainer levels and rosters.
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Fix: Move a trainer in Viridian Gym to prevent getting stuck on spinners.
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Fix: Fix some sprites.
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Fix: Sandstorm and Hail double, not halve, Special Defense and Defense.
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Fix: Enemy Psystrike uses player's Defense.
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Fix: TMs do not refresh PP.
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Fix: Sketch fails if user is transformed.
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Fix: Wild encounter battle transitions correctly depend on relative levels.
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Fix: Dig and Fly prevent capture.
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Fix: Yellow Carpet is buyable.
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Fix: Tangrowth can learn Curse.
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Fix: Lyra's Bag is the female version.
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Fix: Incorrect Cowgirl and Misty sprites.
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Fix: Pokémon caught during the Bug-Catching Contest are recorded as caught in Goldenrod Harbor.
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Fix: Magnet Train tracks were missing tiles.
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Fix: Shiny icon is the star from Gen 3+.
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Fix: SPRITE_DRAGONITE uses Dragonite's side view.
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Remove: Rebattling Breeders like in B2/W2.