Well, the lack of standard layout also means that you'll either be curating an old-style (2002) "symlink farm" which is a tricky sysadmin task, or you'll be searching the new-style (2010) "source registry" which can slow down your startup time by seconds on large code bases.
Why? How about if there are sensible defaults? Common Lisp (or more precisely ASDF) has CL_SOURCE_REGISTRY that almost no one defines and that works great.
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