bug: possibility of writing invalid headers yielding unreadable files

Hey @colinpalmer - as per our discussion:

In juglab/cryoCARE_pip#43 we saw that files were being written, copying the original header but not the extended header. The length of the extended header is stored in the header and as such the start of the data is incorrectly specified in the files `mrcfile` writes.

Proposal: check and update the header entry containing the number of bytes of the extended header when writing a file to avoid this problem in the future

Start by tracing the file-writing path in mrcfile and review the behavior described in juglab/cryoCARE_pip#43. Confirm how the header records the extended-header byte count and define completion as writing files whose header value matches the extended header and whose data starts at the correct offset.

Written by the indexing model from the issue text.