Yes, I understand that it's a nested structure, and that it seems perfectly reasonable to you.
But this number of folders does not seem reasonable to me -- and I only mean it for this mail app (AquaMail), this developer (myself), etc.
AFAIK, there is no Thunderbird for Android.
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About IMAP namespaces. To my knowledge, the only folder which is a special case (lives outside any configured namespace) is the main "default" INBOX.
For others, if you are using a namespace (either manual or automatic setting) -- then you're telling Aqua to only look inside that namespace.
So let's say you have:
Inbox
INBOX.folderA
INBOX.folderB
folderC
and the namespace is "INBOX", then in Aqua you'll see:
Inbox (the folder, not the namespace)
folderA
folderB
(folderC will not appear)
And in fact, Aqua's "LIST" command will then be:
LIST "" "INBOX.*"
where INBOX is the namespace (not the Inbox folder... confusing? to me, yes).
There is no reason for Aqua to go outside the namespace, and it's not desirable to do so (who knows how many thousands of folders there are, at the root level).
Now, Aqua only supports one (first) personal namespace. Sorry. To my knowledge, K9 Mail is the same way.