[C2] Convert file uploads/downloads to OneUpFlySystem

[ywarnier]

This includes reviewing and potentially replacing all call to (non exhaustive list):

• basename()
• chmod()
• chown()
• closedir()
• connection_status()
• copy()
• dir()
• fclose()
• feof()
• file_exists()
• file_get_contents()
• filemtime()
• file_put_contents()
• filesize()
• uses of class Fllesystem()
• fopen()
• fpassthru()
• fread()
• fseek()
• fwrite()
• is_dir()
• is_file()
• link()
• local copyr()
• mime_content_type()
• mkdir()
• opendir()
• pathinfo()
• readdir()
• readfile()
• realpath()
• tempnam()
• rmdir() (and local rmdirr)
• scandir()
• unlink()
• uses of class UploadedFile

We should also check all uses of exec() and system() to see if they do not treat a file path directly.

• exec()
• system()