How does Thunderbird keep track of where it stores your messages?

I am writing a program to isolate certain messages from a messages file. Of course I can hard code the path where the messages are kept at the moment, but when the user changes it, my program will be lost.
I have looked in the registry and profile.ini file with no luck. Anyone knows the answer? Thanks.

The path to messages in Thunderbird is random just for the reason your having trouble. To make programmatic access non trivial.
As you would have observed the profiles.ini contains a path the the root of the profile.
Within the profile mail is stores in profiles\imapmail for IMAP or profiles\mail for pop
Sub folders exist for the server the mail is for, often with a numeric suffix to separate multiple accounts on the same server, or multiple attempts to set up the same account.
These folder can again contain sub folder. depending on the internal structure of folders within Thunderbird.
If the user has specified a custom location for the folder of an account, that information is stored in the prefs.js file along with all other preferences. The account the setting is for is referenced numerically. So you need to establish from the preferences what the account number is, before reading the preference for location.

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