This patch seems to have totally broken the build - aka src folder is used?

indeed

15:30:59  [INFO] Executing tasks
15:30:59  [INFO]      [copy] Copying 693 files to /home/jenkins/agent/workspace/ipse.platform.swt.binaries_PR-65/eclipse.platform.swt.binaries/bundles/org.eclipse.swt.win32.win32.x86_64/src

The ANT tasks of the build copy the OS-dependent source files to the according OS fragment's src folder:

15:30:59 [INFO] Executing tasks
15:30:59 [INFO] [copy] Copying 693 files to /home/jenkins/agent/workspace/ipse.platform.swt.binaries_PR-65/eclipse.platform.swt.binaries/bundles/org.eclipse.swt.win32.win32.x86_64/src

When removing the folder from the build.properties, probably the resulting bundle will be empty and thus the classes cannot be found.

Please dont mess with the buildfiles for SWT as these are build in a special way with ant not maven...