I've noticed some objects are oddly disjointed, like for example the scaffold on the second energy ball puzzle being 90% inside the wall. Is this an issue with the levels or is it an issue with me using the Linux version of Portal (from what i understand the vpks are the same)
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Very strong possibility that I've broken something while adding levels of detail to the different assets that have been used, and not that there was a problem due to using the Linux version of portal (although it's vaguely possible).
Given the pace of development I've had little time to check everything over so I'll file that down as a glitch and see about addressing it when the pressure is off. However getting a good polished game out the end of this really relies on people getting me feedback so thank you so much for posting this, I've added it to the list :D