In autogen.sh add some flags which set useful make options
In autogen.sh etc fix a bug in ProcessOptionsFile

I previously tried to replace `tr '\n' ' '` with a sed command. However
it seems that on some (or all possibly all) machines sed cannot replace
newlines.
Properly handle running autogen from other directories

* Add function to portably get absolute paths

* Use it to get paths for build dir and config file

* Now we can cd to oomph root near the start of autogen
In autogen.sh with -s arg also shut up configure's spam