evandixon

Not quite 100%, but the story's been completed at least.

Ever notice how the majority of command-line applications require about a dozen commands for a single logical operation? This tool aims to fix that! Not only is there an easy-to-use GUI, ROMs can be extracted and repacked with a single console command per operation.

System requirements:
.Net Framework 4.6 Free space on the system drive. Cleanup happens as soon as possible, but especially for larger ROMs, you may need several GB free.
Supported formats for extraction:
Decrypted CCI (aka .3DS) Decrypted CXI (what Braindump gives you) Decrypted CIA NDS ROM
Supported formats for building:
Decrypted CCI (aka .3DS) For use with Citra Can be used for Gateway and Sky 3DS (with CFW) if encrypted using Decrypt9 0-Key Encrypted CCI For use with Gateway CIA For use with CFW HANS RomFS, Code.Bin, and Homebrew Launcher Shortcut NDS ROM
Planned Features:
Copy private header to 0-key encrypted CCI files as they are built. Until this is done, any *.3dz files created are invalid until a private header is added. Credits:
@SciresM for 3DS Builder (modified to use command-line arguments) profi200 for Project_CTR's makerom dnasdw for 3dstool @Asia81 for HackingToolkit3DS, which provided the usage for 3dstool.  
Support Thread & Console Usage

This experimental console application can extract files from NDS ROMs.  The best part is that it's made with .Net Core and is by extension cross-platform (without needing any frameworks to be installed).  It currently cannot rebuild NDS ROMs, but ndstool should be able to accept the files this tool creates.
Usage (Windows):
ToolkitConsoleCore.exe <ROM> <OutputDirectory>
Usage (Linux):
ToolkitConsoleCore <ROM> <OutputDirectory>
Since I don't have a Mac, I can't say what the OSX usage is.
If anyone wants builds for other OS's, I can theoretically provide them if your OS is listed here.
Note: The file size being over 100MB is the result of 8 platform-specific builds being uploaded.  After you click Download, just choose the one you want and the it will only be 20MB max.

Author: @Grovyle91
This is a text editor for Pokémon Mystery Dungeon: Explorers of Time, Darkness, and Sky.

ROM Editor for Pokémon Mystery Dungeon games. Refer to the tutorial for details:
 

Pokémon sprites extracted using GfxCrunch. This 7z contains everything one needs to create animated sprites. It is not intended for humans, as sprites have not been stitched together yet.

Ash's Pikachu
This Pikachu was based on Ash's Pikachu from the anime and was distributed at Toys R Us stores in the USA, Canada, and Puerto Rico.
Wondercard ID 065 PID 933526154 Games DPP HGSS Type Local Wireless Dates 01.31.2011-02.13.2011 Nickname PIKACHU Gender Male Level 50 Nature Naughty Ability Static OT Ash SID 35254 Location Pokémon Event Ribbon Classic Ribbon Ball Cherish Ball Held Item Light Ball Moves Volt Tackle Iron Tail Quick Attack Thunderbolt

Oblivia Deoxys (Attack Forme)
This Deoxys can be sent to any Generation IV game from Pokémon Ranger 3 upon completion of the special Deoxys mission. The mission was distributed via Wi-Fi during the distribution times below. The Forme obtained depends on the results of the mission.
The mission was distributed between Oct 04, 2010 to Jan 11, 2011. The gift could be sent any time, once you completed the Deoxys and the Odd Temple mission.
 
     Species   Attack Deoxys   Nickname (N)   DEOXYS    OT   Oblivia   TID/SID   03060/01859   Distribution   Ranger 3   Location   Pokémon Ranger   Dates   Follows NDS date   PID   Random (Non-Shiny)   Games   Given to: DPPt HGSS 
Preset as: HG                                                                Lv. 50    Nature   Random   Ability   Pressure   Item   (None)    Card Per Save   Only One Allowed    Moves   (ITALIC means Relearnable)   Psycho Boost   Meteor Mash   Superpower   Hyper Beam   WC ID 182: 「Trusted Pokémon Trainer:」  

Classic Trusted Pokémon Trainer: The Ranger Union requests that you
protect this Deoxys. Take care of
this Deoxys well! Format Ver.2.1.2-0, Post Updated Date:20210821_1755

10th Anniversary Mew
This Mew was distributed to HeartGold and SoulSilver games to commemorate the 10th Anniversary of Pokémon Gold and Silver versions. It is the first Pokémon to be distributed with the Premier Ribbon.
Wondercard ID 053 PID Random Games HGSS Type Wi-Fi Dates 10.15.2010-10.30.2010 Nickname MEW Gender Genderless Level 5 Nature Random Ability Synchronize OT FAL2010 SID 39598 Location Wi-Fi Gift Ribbon Premier Ribbon Ball Cherish Ball Held Item --- Moves Pound --- --- ---

Pokémon Ranger Manaphy Egg
This Manaphy egg can be sent from any Ranger game to any Generation IV game after completing the special Manaphy mission. For the first Ranger game, the mission was unlocked with a password. For the second game, the mission was downloadable through Nintendo Wi-Fi from November 10, 2008 to January 31, 2009. For the third game, the mission was downloadable from October 4, 2010 to January 11, 2011.
     Species   Manaphy (EGG)   Nickname   Egg (save lang)   OT   (recipient)   TID   (recipient)   Distribution   Mission Reward   Location   Pokémon Ranger   Dates   (sent from Ranger)   PID   Chance of Shiny 
(when hatched in different game)   Games   DPPTHGSS                                                                Lv. 1    Nature   Random   Ability   Hydration (1 or 2)   Item   None    Moves       Tail Glow   Bubble   Water Sport   (None)

   (no ribbons) Format Ver.1.0.6-3, Post Updated Date:20190104_2346

Alamos Darkrai (Australia) This Darkrai was distributed at various retail stores in Australia as a promotion for the release of the 10th anime movie.
Wondercard ID 011 PID Random Games DP Type Local Wireless Dates 10.30.2008-11.09.2008 Nickname DARKRAI Gender Genderless Level 50 Nature Random Ability Bad Dreams OT ALAMOS SID 61209 Location Pokémon Event Ribbon Classic Ribbon Ball Cherish Ball Held Item Moves Roar of Time Spacial Rend Nightmare Hypnosis

Pokétopia Electivire
This Electivire can be sent to any Generation IV game from Pokémon Battle Revolution after entering the password BA16-X4SH-E2AT as your Self Introduction.
* It is known that this gift does not have the flags for PtHGSS, however given Pokémon Battle Revolution injects the wonder card directly into the game save, the receiving flags does not matter. Video showing Electivire being received on Platinum (another PBR -> main series event), credits to Randomdice101.
     Species   Electivire   Nickname (N)   ELECTIVIRE    OT   PKTOPIA   TID/SID   06257/47618   Distribution   In-Game Gift   Location   Lovely place   Dates   Starting June 25th, 2007   PID   D7345A6 (Non-Shiny)   Games   Given to: DP PtHGSS*
Preset as: D                                                                Lv. 50    Nature   Adamant   Ability   Motor Drive   Item    Magnet    Card Per Save   Only One Allowed    Moves   (ITALIC means Relearnable)   Thunder Punch   Ice Punch   Cross Chop   Earthquake   WC ID 151: 「Shocking Secret Gift」  

   (no ribbons) Shocking Secret Gift This is a special Secret Gift.
You can receive a powerful,
Electric-type Pokémon! Try out
this Pokémon in battle! Format Ver.3.0.1-5, Post Updated Date:20240316_1515

Pokétopia Magmortar
This Magmortar can be sent to any Generation IV game from Pokémon Battle Revolution after entering the password B416-X4HT-VTWF as your Self Introduction.
* It is known that this gift does not have the flags for PtHGSS, however given Pokémon Battle Revolution injects the wonder card directly into the game save, the receiving flags does not matter. Video showing Electivire being received on Platinum (another PBR -> main series event), credits to Randomdice101.
     Species   Magmortar   Nickname (N)   MAGMORTAR    OT   PKTOPIA   TID/SID   06257/02565   Distribution   In-Game Gift   Location   Lovely place   Dates   Starting June 25th, 2007   PID   D71BF12 (Non-Shiny)   Games   Given to: DP PtHGSS*
Preset as: D                                                                Lv. 50    Nature   Modest   Ability   Flame Body   Item    Charcoal    Card Per Save   Only One Allowed    Moves   (ITALIC means Relearnable)   Flamethrower   Psychic   Hyper Beam   Solar Beam   WC ID 152: 「Heated Secret Gift」  

   (no ribbons) Heated Secret Gift This is a special Secret Gift.
You can receive a powerful,
Fire-type Pokémon! Try out
this Pokémon in battle! Format Ver.3.0.1-5, Post Updated Date:20240316_1513

Alamos Darkrai (Netherlands) This Darkrai was distributed at the Pokemon Day event at the Walibi World theme park in the Netherlands as a promotion for the release of the 10th anime movie.
Wondercard ID 010 PID Random Games DP Type Local Wireless Dates 08.30.2008-08.31.2008 Nickname DARKRAI Gender Genderless Level 50 Nature Random Ability Bad Dreams OT ALAMOS SID 22261 Location Pokémon Event Ribbon Classic Ribbon Ball Cherish Ball Held Item Moves Roar of Time Spacial Rend Nightmare Hypnosis

Pokétopia Surfing Pikachu
This Surfing Pikachu can be sent to any Generation IV game from Pokémon Battle Revolution after completing the game.
* It is known that this gift does not have the flags for PtHGSS, however given Pokémon Battle Revolution injects the wonder card directly into the game save, the receiving flags does not matter. Video showing Electivire being received on Platinum (another PBR -> main series event), credits to Randomdice101.
     Species   Pikachu   Nickname (N)   PIKACHU    OT   PKTOPIA   TID/SID   06257/44870   Distribution   In-Game Gift   Location   Lovely place   Dates   Starting June 25th, 2007   PID   19D97C13 (Non-Shiny)   Games   Given to: DP PtHGSS*
Preset as: D                                                                Lv. 10    Nature   Hardy   Ability   Static   Item    Light Ball    Card Per Save   Only One Allowed    Moves   (ITALIC means Relearnable)   Volt Tackle   Surf   Tail Whip   Thunder Wave   WC ID 150: 「Secret Gift」  

   (no ribbons) Secret Gift Use PIKACHU’s Surf
in Pokémon Battle Revolution
and see PIKACHU ride on
a surfboard. Format Ver.3.0.1-5, Post Updated Date:20240315_2055

Winter Suicune
The shiny Johto beasts were distributed as a tie-in with the thirteenth movie and to promote the upcoming Black and White versions. When sent to a Black or White game via the Relocator, any of the three beasts can activate an event to meet, battle and catch Zoroark in Lostlorn Forest.
   Species   Suicune   Nickname (N)   SUICUNE    OT   WIN2011   TID/SID   02211/01980   Distribution   Nintendo Network   Location   Pokémon Event   Dates   Feb 21 to Feb 27, 2011   PID (Specified)   7AE975F0 (Shiny)   Games   Given to: DPPt HGSS 
Preset as: HG                                                                Lv. 30    Nature   Relaxed   Ability   Pressure   Item    Rowap Berry    Card Per Save   Only One Allowed    Moves   (ITALIC means Relearnable)   Sheer Cold   Air Slash   Extreme Speed   Aqua Ring   WC ID 61: 「The Legendary Trio of Johto!」  

Classic The Legendary Trio of Johto! Transfer your Shiny SUICUNE to Pokémon
Black Version or Pokémon White Version
for a special encounter! Be sure to
save the game once you receive SUICUNE
at a Poké Mart. Format Ver.2.1.2-0, Post Updated Date:20210821_1750

Alamos Darkrai (UK) This Darkrai was distributed at Woolworths stores in the UK as a promotion for the release of the 10th anime movie.
Wondercard ID 009 PID Random Games DP Type Local Wireless Dates 08.06.2008-08.31.2008 Nickname DARKRAI Gender Genderless Level 50 Nature Random Ability Bad Dreams OT ALAMOS SID 45156 Location Pokémon Event Ribbon Classic Ribbon Ball Cherish Ball Held Item Moves Roar of Time Spacial Rend Nightmare Hypnosis

VGC Shiny Eevee
This shiny Eevee was distributed at regional matches for the Pokémon Video Game Championships. There were various distributions between May 08 to Jun 28, 2010.
   Species   Eevee   Nickname (N)   EEVEE    OT   VGC10   TID/SID   05080/49497   Distribution   Local Wireless   Location   Pokémon Event   Dates   (Various)   PID (Specified)   5FEF8D69 (Shiny)   Games   Given to: HGSS 
Preset as: HG                                                                Lv. 50    Nature   Hardy   Ability   Adaptability   Item    Focus Sash    Card Per Save   Only One Allowed    Moves   (ITALIC means Relearnable)   Iron Tail   Trump Card   Flail   Quick Attack   WC ID 52: 「Wow! Shiny EEVEE!」  

Classic Wow! Shiny EEVEE! Thanks for coming to a 2010 Pokémon
Video Game Championships event!
Be sure to save your game after you
pick up the Pokémon at the Poké Mart. Format Ver.2.1.2-0, Post Updated Date:20210821_1759

Ash's Pidove
The Secret Eggs were distributed at Toys R Us stores in the USA to commemorate the main character getting an egg in the anime. The three Pokémon are based on the anime characters' Pokémon. Each player could receive one at random. This Pidove always has an Attack IV of 31.
     Species   Pidove (EGG)   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Local Wireless   Location   Pokémon Event   Dates   Apr 27 to May 31, 2011   PID   Cannot Be Shiny   Games   BW                                                                Lv. 1    Nature   Hardy   Ability   Super Luck (2)   Item   (None)    Card Per Save   Only One Allowed    Moves   (ITALIC means Relearnable)   Gust   Quick Attack   Air Cutter   (None)   WC ID 1D: 「A Secret Egg!」's receiving text 0x44 Thank you for playing Pokémon! Please pick up your gift from the deliveryman in any Pokémon Center.

   (no ribbons) A Secret Egg! What Pokémon will hatch from
this Egg? Keep it with you
on your journey and take care
of it, and you'll find out! Format Ver.2.1.1-2, Post Updated Date:20210820_1201

Alamos Darkrai (USA) This Darkrai was distributed as a promotion for the release of the 10th anime movie. It was first distributed from May 31 to June 1 at Toys R Us stores in the US, then from June 1 to June 30 at the Nintendo World store in New York City.
Wondercard ID 007 PID Random Games DP Type Local Wireless Dates 05.31.2008-06.30.2008 Nickname DARKRAI Gender Genderless Level 50 Nature Random Ability Bad Dreams OT ALAMOS SID 10413 Location Pokémon Event Ribbon Classic Ribbon Ball Cherish Ball Held Item Moves Roar of Time Spacial Rend Nightmare Hypnosis

Iris's Axew
The Secret Eggs were distributed at Toys R Us stores in the USA to commemorate the main character getting an egg in the anime.
The three Pokémon are based on the anime characters' Pokémon. Each player could receive one at random.
This Axew always has a Speed IV of 31.
 Species   Axew (EGG)   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Local Wireless   Location   Pokémon Event   Dates   Apr 27 to May 31, 2011   PID   Cannot Be Shiny   Games   BW    Lv. 1                                                                  Nature   Naive   Ability   Mold Breaker (2)   Item   None      Moves       Scratch   Dragon Rage   (None)   (None)   WC ID 29: 「A Secret Egg!」's receiving text 0x44 Thank you for playing Pokémon! Please pick up your gift from the deliveryman in any Pokémon Center.

Movie 2011 Victini
This Victini was distributed to promote the pair of 14th Pokémon movies along with several other Victini merchandise and game promotions.
The gender of the OT is determined by the gender of the player.
The first distribution was advertised to US players, while the second distribution was advertised to UK players.
 
 Species   Victini   Nickname   (default, save lang)   OT   Movie14   TID   12031   Distribution   Online Wi-Fi   Location   Wi-Fi Gift   Dates   Dec 03, 2011 
to Jun 12, 2012   PID   Cannot Be Shiny   Games   BW    Lv. 50      Nature   Random   Ability   Victory Star (1)   Item   Fire Gem 
Wishing   Moves       V-create   Fusion Flare   Fusion Bolt   Searing Shot   WC ID 32: 「Virtuoso Victini!」's receiving text  0x44 Playing Pokémon

Almia Darkrai This Darkrai can be sent to any Generation IV game from Pokémon Ranger 2 upon completion of the special Drakrai mission. The mission was distributed via Wi-Fi during the distribution times above.
Wondercard ID 022 PID Random Games DPP HGSS Type Ranger 2 Dates 12.01.2008-01.31.2009 Nickname DARKRAI Gender Genderless Level 50 Nature Random Ability Bad Dreams OT Almia SID 46999 Location Pokémon Ranger Ribbon Classic Ribbon Ball Poké Ball Held Item --- Moves Dark Void Dark Pulse Shadow Ball Double Team

Plasma Deoxys
This Deoxys was distributed to Black 2 and White 2 games via Nintendo Wi-Fi Connection.
 
 Species   Deoxys   Nickname   (default, save lang)   OT   Plasma   TID   05083   Distribution   Online Wi-Fi   Location   Lovely place   Dates   May 08 to May 31, 2013   PID   Cannot Be Shiny   Games   : B2W2    Lv. 100      Nature   Random   Ability   Pressure (1)   Item   Life Orb 
Classic   Moves       Nasty Plot   Dark Pulse   Recover   Psycho Boost   WC ID 133: 「It's Deoxys!」's receiving text  0x44 Playing Pokémon

Plasma Genesect
This Genesect was distributed via Wi-Fi to players who purchased Black 2 or White 2 during the first month of its release.
This was the first time Genesect was released to English games.
 
 Species   Genesect   Nickname   (default, save lang)   OT   Plasma   TID   10072   Distribution   Online Wi-Fi   Location   Wi-Fi Gift   Dates   Oct 07 to Nov 12, 2012   PID   Cannot Be Shiny   Games   B2W2    Lv. 15      Nature   Random   Ability   Download (1)   Item   None 
Classic   Moves       Techno Blast   Magnet Bomb   Solar Beam   Signal Beam   WC ID 99: 「The Mythical Pokémon Genesect!」's receiving text  0x44 Playing Pokémon