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Those apps are written in .NET and are compiled to CIL, which is easily decompilable with a tool such as ILSpy or the Mono disassembler
For open-source tools, Project CTR includes ctrtool to extract many 3DS formats including CIA, and makerom to build an NCCH, CIA, or CCI file. It's a bit old so I'm not positive it'll work exactly, but there's a guide on extracting a CIA using ctrtool and 3dstool, then rebuilding it using makerom and 3dstool.
For open-source tools, Project CTR includes ctrtool to extract many 3DS formats including CIA, and makerom to build an NCCH, CIA, or CCI file. It's a bit old so I'm not positive it'll work exactly, but there's a guide on extracting a CIA using ctrtool and 3dstool, then rebuilding it using makerom and 3dstool.
For open-source tools, Project CTR includes ctrtool to extract many 3DS formats including CIA, and makerom to build an NCCH, CIA, or CCI file. It's a bit old so I'm not positive it'll work exactly, but there's a guide on extracting a CIA using ctrtool and 3dstool, then rebuilding it using makerom and 3dstool.
I'm not sure if there's an existing open-source tool for creating CIA files of GBA games. A lot of focus has moved to open_agb_firm, which allows running GBA ROMs directly using the native hardware support, and has many advantages over the official implementation.