I noticed this when investigating an aerc bug report [1]. When the notmuch config contains a different location for database.mail_root (e.g. ~/.mail/user) and database.path (unset, should default to ~/.local/share/notmuch/default), the filepath returned by "notmuch_message_get_filename" points to the database path instead of the mail_root path. Here is a simple reproduction in python [2], that uses the problematic "notmuch_message_get_filename". "notmuch show" on the other hand does have the correct filename/path.
[1]: https://todo.sr.ht/~rjarry/aerc/106 [2]: https://paste.xenrox.net/~xenrox/d7048c7b5392df940586b42673aeba97c176d489
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