I have a google apps account and want to have access to my gmail emails through this account. Is there a way, I can merge the accounts or move the emails from gmail to google apps account as soon as they arrive?
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You could synchronize both mailboxes using imapsync.
Either you do that regularly or you synchronize the mailboxes once and then setup a mail forwarding in your GMail account to your Google Apps account, see Forwarding mail to another email account automatically.
I'd go with the second option.