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With all of Gmail's changes, I've lost the ability to file my emails into my created labels. Instead, they now stay in my inbox, with the named label listed on the subject line; thus voiding the point of my labels and making the only way to thin my inbox is to delete.

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You need to "Archive" the messages. That removes them from the Inbox but does not affect any other labels that have been applied. – Al E. May 16 '12 at 18:49
@JUDY Never delete emails in Gmail. Many people have been confused by the Archive button. The archive removes the inbox label from the conversation. If it has another label you are good to go. If it doesn't have a label it is still in "all mail" – mhoran_psprep May 17 '12 at 1:37

I have filters that labels emails and to get them out if the inbox you have to mark the option (when creaing the filter, or editing the exitsings that you have) "skip inbox", so they will go directly to the label.

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