Since our site was founded, we at Project Pokemon have asked that people distribute ROM hacks using patches (such as IPS or XDelta), and not by directly distributing modified ROMs, not even individual files within them. This is because copyright law prohibits the distribution of copyrighted works, bringing stiff penalties for anyone who does so anyway. Using patches, it is possible to only distribute the modifications and not the copyrighted bits.
This worked nicely for GBA and NDS games, because all GBA and NDS roms are essentially identical to each other (mostly), regardless of how they are dumped. Things got more complicated with 3DS games, however. There are a variety of different formats for 3DS ROMs that don't always store the exact same information, so traditional patching methods won't work. Some people made patches for just the romfs and exefs portions of ROMs, which for the most part works, but is rather inconvenient for the end user. That's when I created the DS ROM Patcher, an easy-to-use tool designed to make this whole process simpler. Using this tool, an easy-to-use zip file contains all the tools and patches needed to use a ROM hack. It accepts decrypted ROMs in a variety of formats, and can output ROMs in a variety of formats.
As the 3DS hacking scene progressed, eventually LayeredFS was invented, and it became possible to just distribute all the modified files in an easy to use zip file without the need for additional tools. While this is undoubtedly the most convenient way to use ROM hacks, it's not exactly the most legal. Copyright law not only prohibits distributing copyrighted works, but it also forbids distributing portions of these works too. For some 3DS games it may not be an issue, as a single small file can be replaced rather easily, but most ROM hacks distributed on this site are for the mainline Pokemon games developed by Game Freak. Instead of containing individual files, these games contain obfuscated archives each containing hundreds of smaller files. When using LayeredFS, changing even one of the files within requires distributing the entire archive. Changing several files from across different archives results in needing to distribute a significant portion of the original ROM, and with each file it steps closer and closer to distributing the whole ROM.
Because distributing entire ROMs has always been against the rules at our site, we decided to not allow hacks to be distributed in this way any longer. We have deleted links to ROM hacks that were already distributed this way, but because of the widespread use, no one will get any closer to a ban unless they do so after having been directly told. We are not banning 3DS ROM hacks, as there are still legal ways to distribute them, like the DS ROM Patcher. No one is required to use this tool (if you have an alternative, I encourage you to bring it up), but no one is allowed to distribute whole modified files as is commonly done with LayeredFS.
If anyone has any questions, comments, or concerns, please create a thread in the Feedback forum or send me a private message. If anyone has any concerns about my tool, the DS ROM Patcher, please let me know here.