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Multiple selection window pops up when you want to select input layer(s) within Processing Tools.

The order of layers in Multiple selection window seems not corresponding to Layer Panel.

How to sort out the layer list in QGIS Multiple selection window?

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This is fixed in QGIS 3.0 - I don't believe there's plans to change the 2.x releases correspondingly

  • Thanks. That's great news! So I will try some dev nightly while waiting the release date next two week. – sandthorn Feb 12 '18 at 8:23

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