Previously, VFS::open() would only use the passed flags for permission checking
purposes, and Process::sys$open() would set them on the created FileDescription
explicitly. Now, they should be set by VFS::open() on any files being opened,
including files that the kernel opens internally.
This also lets us get rid of the explicit check for whether or not the returned
FileDescription was a preopen fd, and in fact, fixes a bug where a read-only
preopen fd without any other flags would be considered freshly opened (due to
O_RDONLY being indistinguishable from 0) and granted a new set of flags.
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