OK, the particular version of dwi2fod you’re using dates back from 11 Dec 2015 (this commit) - the current version is 0.3.15-535-g21da6244. Your version predates the changes that were made to bring the MSMT-CSD method into the dwi2fod command, which explains the error message.
As to why you’re using an old version despite a recent git pull, my guess is that your previous install used the old PATH setting, which used to be {mrtrix3_folder}/bin. This changed with version 0.3.14 so that executables are now located in {mrtrix3_folder}/release/bin (as detailed in this post at the time). So if you haven’t updated your PATH, you’d still be using the executables left over from the previous installation, despite having just compiled the new ones… You should nowadays be able to use the ./set_path command from the mrtrix3 folder to set that up correctly. I also recommend you remove the previous export PATH=... line from your ~/.bashrc file to avoid further conflicts, and rely on the ./set_path command to update it from now on. I also recommend you remove the bin/ folder and all of its contents to make sure you genuinely are using only the most recent executables.
Incidentally, we are about to revert to the previous PATH location within the next few days, when we release a major update… I won’t go into the details of why these changes were made (it’s a long story), but hopefully reverting to {mrtrix3_folder}/bin will cause less confusion in the future - and we won’t be changing it again in a hurry…