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Do we need database.inc.php & database_mysqli.inc.php or only one?

Also with email piping & smtp can we disable/remove the pop3 and imap files?

Technically, you only need one of the database files as far as I know (as you will be connected to your database only via MySQL or MySQLi - never both at the same time).... but there's no benefit to deleting the extra file. Same goes with the pop3 and imap files. They're not needed if you're not using them, but there's also no major benefit to deleting them (unless you need the extra couple hundred KBs of space )

No just looking at everything down to the millisecond

What Mike said.

Hesk will use the improved MySQLi functions to access the database. For legacy reasons (to support some older PHP versions), the alternative mysql functions are available.

You can indeed delete the fetching files you aren't using.

ok, so the question still remaining is, with the email piping (incoming?) and smtp (outgoing) is imap still needed?

No, IMAP is just one of the 3 available options to do the same thing: import emails into tickets.

So you need either email piping, POP3 fetching or IMAP fetching.