Here's some tips for a few possible compiling issues.
--for cubic ninja compilation, you need blowfish_processed.bin and blz.exe in the scripts folder.
Find the blowfish file online at an iso site or google pastebin and the file name. Then copy the contents of the paste and ... paste them inside your favorite hex editor and save. The resulting md5 should be: 33f38ab6f0821bc64b6f6bf98c1494f0
The blz.exe file is an obscure DS homebrew tool and I had a hell of a time tracking it down. I've attached it below inside the sslpatcher package.
--you need to use the libctru in the repo - it's a really old one. Just put export CTRULIB=<path to your ninjhax2.x repo>/libctru near the beginning of the root makefile.
--do not type "make". you need to install pythonX.X and input something like (for example):
python scripts/buildVersion.py "9.2.0-20U" OR python scripts/buildAll.py
You can also add --enableotherapp to get otherapp payloads. See oothax3d readme for information on those.
The resulting payloads (cubic ninja and otherapp) will be in the p/ directory, QRs in the q/ directory, and ropbins (for menuhax) in r/ directory.
--you need ARMIPS.exe somewhere in your path. You can find it
here. (speaking of which,
@d0k3 , could you add blz.exe? thx!)
There may be other tips I'll add later, and I'll answer questions if I can.