When sending an email via Mantis email api, the In-Reply-To header is treated differently from the others: the value provided is concatenated with the hostname and enclosed in angular brackets (see email_api.php, function email_send() at lines 1422 and following). This prevents setting a custom In-Reply-To.

To provide a use case, I'm currently implementing a "issue created" acknownledgment in Email Reporting plugin. Being the aknowledgement email a response to the reporter's one, I need to send it with In-Reply-To field containing the original Message-ID, as per rfc822. The reporter's email MessageID may not come from the same server Mantis is installed on, so it may have a different hostname.

The most right solution could be simply removing the relevant case, allowing to specify the full header, like this: https://github.com/penguin86/mantisbt/commit/e8a6d5f608bf72817d6fb16f55b3982997cc91cd
For what I can see, the only place where it is used in Mantis is in email_bug_info_to_one_user() (email_api.php:1682), that should be changed to include the hostname (maybe refactoring the code used to obtain the hostname, see email_api.php:1190, in a function?).

But this may eventually break the plugins using that header (are there any?), so another solution could be check for the <>@ symbols and add the hostname only if not already present, like here: https://github.com/penguin86/mantisbt/commit/59d73376a129d72442970f6c72afed29fc861f9f

Please let me know which solution you find accettable, so I can submit a pull request.

Thank you very much!