I have always wished that LyX would put the compiled PDF files in the same folder as the .lyx file. This seems like the only natural way to do it since you need to find that file to share with your colleagues. One never shares LyX files. It should at least be a simple option to set in the settings.
On the other hand, LyX's actual behavior is to put the PDF file in a temporary folder with a nearly impossible to know name. This makes life difficult for almost everyone. There is an inconvenient workaround at " https://tex.stackexchange.com/questions/71110/can-lyx-automatically-save-the-pdf-output-in-the-same-folder", but that doesn't really address the fundamental design problem.
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