Build/compilation update

Fixed build on GCC4.7, Linx Mint (missing unistd include).
Fixed build on GCC4.2.1, OS X 10.7 (change in generated file name).
Updated ignore to cover new temporary build files.
Enforce minimum automake version

Due to changes in the name of bison generated files, only automake
version 1.12.1 and higher are now supported.