Well, for one, the logging doesn't work the way it used to when a build project is Aborted. Here's the short version:
We run our project from the command line. It runs continuously. Before, a person could close the window while the continuous integration build project was in "sleep mode", causing the build to end and the next build cycle would log just fine. W/the beta, whenever the build is stopped, the next build cycle's "Transform Log File" step would Fail because of missing xml elements, which is what the transform step is suppose to add. I didn't look too close at it though.
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