clean_header: Write to correct dst_file

Write to correct dst_file when in update mode. This enables use cases
like the following:

../../../bionic/libc/kernel/tools/clean_header.py -k original-kernel-headers/ -d kernel-headers/ -u linux/ion.h

Previously, we had to cd into kernel-headers/ and then run

../../../../bionic/libc/kernel/tools/clean_header.py -k ../original-kernel-headers/ -d . -u linux/ion.h

because the tool didn't allow the relative path to be different from the
destination path.

Change-Id: I8c5e284ce7a6737d77a2f5ead3e7e5db01317425