James Zern e9b7f98c56 Revert "vp9: Avoid encoder loopfilter for non-reference frames."
This reverts commit 863f860bfcf3bdc26eeecb299aa481d0f63d11ac.

This causes encoder / decoder mismatches in various
VP9/DatarateTestVP9Large.BasicRateTargeting3TemporalLayers tests

BUG=webm:1408

Change-Id: Ic200c39d7ed9c0b0247ef562f5d6f7b2625f7e14
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