How to access and auto process some mails depending on content?

Hello, i auto process some mails depending on content. Currently i manually save mails into a folder as plain text files using an add-on. That folder is periodically scanned by my tool and some mails are auto processed, extract information and delete so far. I want to do more and create auto replies depending on mail content in the future. Furthermore processed and deleted mails must be removed from my mail account. And i dont want to select and manually extract all those mails that can be processed automatically. Thus i need Thunderbird to somehow store all mails in a directory. Which my tool will scan periodically. The file format is less important (eml, html or txt), i can find a way to process it. I found some information about Maildir in Thunderbird. Tested it, but while the header is always readable the text body is often not. Im stuck at that point. I am not sure how to continue. Maybe i have approached it all badly. The addon im using to export mails is ImportExportTools NG from Christopher Leidigh, its doing a great job but even if i find a way to auto extract all mails it would be painful to sync back deletion actions, not to mention auto replies. I hope someone here can give me a hint on how auto processing of mails is done by companies and how i might do it. I know deletion based on filters can be done with Thunderbird, but this is only the easiest tasks. I plan to do way more, it will be a continuous project, always adding new rules for auto processing specific mails.