Well, the problem with uppercase letters will be that some file systems (e.g. NTFS) ignore them and treat filename.txt and FILENAME.TXT as the same file, while other file systems (for example, I think ) think of it as 2 different files.
So, if you have a link to a file that you named file.txt, and links point to a File.txt file, then NTFS is not a problem, but if you copy files to the file system as ext, the link will not work, because the file system thinks that there is no such file as File.txt.
Because of this, lowercase letters are best used.
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