Jimmy,
No problem. I'm still pretty new at this. I'm happy to share as I'm working through this, although that means that my first response may not be the best or most thorough one.
For example, now that I've got a bit more time into this, I see that cwoz and I both had the same misunderstanding. We both interpreted the book (p.17) to say that we should type:
./.gradlew setupDecompWorkspace
I see now that the second period was the end of a sentence (oops!), and we were supposed to type:
./gradlew setupDecompWorkspace
Although it certainly does work to use the full path name, it also (usually) works to use "./".
I did run into an out of memory problem on one of my Macs, and had to adjust the heap space. To do this I edited the gradlew.bat file, and changed the line that says:
%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS%... (etc.)
to read:
%JAVA_EXE%" -Xmx512m
%DEFAULT_JVM_OPTS% %JAVA_OPTS%... (etc.)
Another tidbit: I ran "./gradlew" before running "./gradlew setupDecompWorkspace". I haven't tested whether it works without running "./gradlew" first...
Regarding the missing items: It turns out that they are misplaced rather than missing. On page 28 the book shows a picture from the Eclipse window. There are a number of files shown directly underneath "JRE System Library" which didn't show up there on my Mac. In my eclipse window there is a folder named "Referenced Libraries" directly underneath "JRE System Library". It turns out that the files are all in there. I'm not sure why this is true (maybe the Forge version?), but it all does seem to work. (I have now moved well past chapter 3.)
BTW, thank you for creating this book. It is full of valuable information. :)
MN