Let me just say that Jenkins isn't as easy to setup on Windows. You probably already knew that.
As an overview, this is the high-level way we write and build code and what is needed for continuous integration:
1) Java 7 and 8
2) Eclipse or IntelliJ for writing code and running tests outside the command line or Jenkins
3) Maven 3x
4) GIT 1.8.4 on Mac, GIT (msysgit 1.9.2) on Windows
5) Jenkins master running on Linux.
6) Jenkins slave agent running as a slave app on Windows
7) Cygwin for windows
Further problems encountered setting up Jenkins on Windows 2012, besides what I detailed in prior post.
1) SH scripts for running tests need to run on Windows
2) Access denied issues when running certain files (e.g BAT)
3) CreateProcess from Jenkins cannot find files to run
The first issue above is that we use SH scripts (in Bash) to setup testing and run our tests after all other packages are built. Windows won't recognize SH scripts as runnable. I decided that since I had Cygwin installed with Bash I could launch these SH scripts from within a BAT file.
The BAT file is basically one line:
C:\cygwin64\bin\bash.exe --login "C:\jenkins\workspace\...\deployScript.sh"
I originally had it start with bash, but the process couldn't be found when done through Jenkins, since it was launched through CreateProcess. I solved my 3rd issue above by fully qualifying what process I wanted to kick off under cygwin with the full path of where bash lived, and I was done with my BAT script.
The 2nd issue above was seen in build failures inside of Jenkins runs where I would see access denied. I thought I could change permissions in the POM files where these scripts were launched but that didn't work.
Ultimately, I found that access denied with my scripts was caused by Eclipse. Eclipse wouldn't make some of the new files I created executable. I clicked on properties and updated the scripts to make them fully executable, and had no further issues.