When I upload a folder and a file together from the Web interface through drag-and-drop, the file turns out to be inside the folder.
Just to give you a concrete example. Suppose we have following files
/test1
/test1/test1.txt
/test2.txt
After uploading, they become
/test1
/test1/test1.txt
/test1/test2.txt
The testing environment:
Seafile-pro-server-6.0.7
Browser Chrome Version 55.0.2883.87 (64-bit)
OS: Kubuntu-14.04