MakeGood doesn't seem to work for versions later than Indigo (3.8).
Example commandline generated by MakeGood in Indigo:
/usr/bin/php -c /tmp/zend_debug/session5741147879914839410.tmp/php.ini -d asp_tags=off -d short_open_tag=on /home/dev/.eclipse/org.eclipse.platform_3.8_155965261/plugins/com.piece_framework.makegood.stagehandtestrunner_2.5.0.v201311031709/resources/php/bin/testrunner.php --no-ansi phpunit -p /home/dev/workspace/Acme/app/bootstrap.php.cache --log-junit=/tmp/com.piece_framework.makegood.launch/MakeGood1399206591471.xml --log-junit-realtime --phpunit-config=/home/dev/workspace/Acme/app/phpunit.xml.dist -R --test-file-pattern=Test(?:Case)?\.php$ /home/dev/workspace/Acme/src/Yuav/AcmeBundle/Tests
And in Juno/Kepler/Luna:
/usr/bin/php -c /tmp/zend_debug/session3820024215614976335.tmp/php.ini -d asp_tags=off -d short_open_tag=on /home/dev/workspace/Acme/src/Yuav/AcmeBundle/Tests/Controller/JobControllerTest.php --no-ansi phpunit -p /home/dev/workspace/Acme/app/bootstrap.php.cache --log-junit=/tmp/com.piece_framework.makegood.launch/MakeGood1399206154221.xml --log-junit-realtime --phpunit-config=/home/dev/workspace/Acme/app/phpunit.xml.dist -R --test-file-pattern="Test(?:Case)?\.php$" /home/dev/workspace/Acme/src/Yuav/AcmeBundle/Tests
As you can see, testrunner.php is never called - and bootstrap is never triggered regardless whether it's defined or not.
For your error in particular, I'm guessing it's your autoloader is not triggering, due to the lack of bootstrapping
You can use a workaround by setting php executable to a bash script hardcoding the path to testrunner.php
#!/bin/bash
# MakeGood for PHP stopped working after Eclipse Indigo (3.8) due to inability to run testrunner.php
# This is a hack PHP binary, to be configured as PHP executable for MakeGood to start working in Juno, Kepler and Luna.
# Remove the -n operator to read all config files
options=`echo $@ | sed 's%-n %%' | sed 's%-c .+? %%'`
# Hardcode path to testrunner.php
options=`echo $options | sed 's@open_tag=on [^ ]*@open_tag=on /opt/testrunner.php@'`
/usr/bin/php $options