In the Properties->C/C++ Build->Settings->Tool Settings tab, the configure and autogen.sh options are specified. While the user can change the values of the command (e.g. configure to myconfigure), these changes are not honored during the build.
A fix has been made.
eclipse-cdt-4.0.1-3.fc8 has been pushed to the Fedora 8 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update eclipse-cdt'
eclipse-cdt-4.0.1-3.fc8 has been pushed to the Fedora 8 stable repository. If problems still persist, please make note of it in this bug report.