Add external ID mode for update-from-file#135
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This is a breaking change because it removes the `--update-file` option. The option is always assumed true for `update-from-file` and is always false in `add-from-file`. The behaviour of these two commands have changed slightly, users are encouraged to read the updated help texts. refer: #134
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This PR adds support for external IDs in update-from-file, cf. #134. It also adds the option
--link-duplicates.