> Makes sense. The problem is actually more complicated than I expected. In my case, I have a system bioinfo.layout under .lyx/layout, without system bioinfo.cls. I have newer version of bioinfo.layout and bioinfo.cls locally.
Problem 1: Currently, lyx will not find local bioinfo.layout and .cls because the entry in textclasslist is used, which says bioinfo.cls is unavailable. I think local layout files, instead of system ones, should be used when a local layout exists. Problem 2: In case there is a local .layout file, existence of .cls is not checked. Problem 3: If I do not have local bioinfo.layout, but with local bioinfo.cls. Lyx->reconfigure will not find it (bioinfo.cls not in $TEXINPUT), and local .cls will not be used. So, ideally, local .layout should be used if available, and the availability of .cls should be checked (local or $TEXTINPUT) if textclass is not found (problem 3) or .layout is found locally (problem 2). However, checking the availability of .cls is nontrivial. (Basically, I need to create a simple .tex file and run latex ...) These problems can be WONTFIX for 1.5.x, but have to be fixed for 1.6.x because embedded .lyx files make heavy use of local .layout and .cls. Cheers, Bo
