>>>For some time I have been using an application called Smartserver which connects to an email pop server and retrieves the emails and files them all separately as text files in a given folder. Sadly this is a 16 bit application and I need to find a replacement - any ideas?
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>>Thunderbird files emails separately.
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>I can find the profiles directory but how how do I tell Thunderbird to file the incoming mail into a folder of my choice automatically?

you can set up rules, which in the older german version I use is under extras/filter.
AFAIK Thunderbird uses SQLite as database, so you might try from that angle to export.