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I can't seem to find a tool to merge files from the active TOC into one file...

The datamanagement --> Merge Shape files only allows you to choose a directory of shapefiles to merge which is really inconvenient as you then have to place only the required files in one directory etc or use the "select by layers" and then choose files which is a pain if the files are in multiple directories.

The Geoprocessing Tools --> Difference on the other hand just lets you choose files from a drop down of files in the TOC. This is so much easier.

Is there a version of merge in QGIS that works like "Difference"?

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MMQGIS "Merge Layers" tool should do it.

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