updating Machinekit

Today I thought that I would update Machinekit from 09-02 build to latest version so, ran instructions on site
cd ~/linuxcnc/src
git pull origin
make

downloaded ok with lots of renames

but make gave an error
make: Entering directory `/home/linuxcnc/linuxcnc/src'
*** configure.in has changed ***
Not running autoconf to avoid tainting universal build
Please investigate or start from scratch:
./autogen.sh && ./configure --your-configure-args...

As I do not know what args were used originally can tell me what they should be.
Thanks
Alan