After successfully building spigot with build tools, I moved the directory to a different one and rebuilt again. Everything ran well until patching started. During patching, a number of errors referencing the old directory appeared, such as "fatal: 'c:/Users/Mooman/Desktop/New folder/CraftBukkit' does not appear to be a git repository".

Here is the tail of the log,
https://gist.github.com/mooman219/8be2079b3d2708c89fef