Merge pull request #495 from mantidproject/11429_stitch1dmany_overwrites_output

I tested the changes running this slightly modified usage example, which puts each of the workspaces into a WorkspaceGroup first. Without these changes the two resulting WorkspaceGroups contain the same workspace (the first one is overwritten), after the changes this does not happen, as described in the ticket.

```
trans1 = Load('INTER00013463')
trans2 = Load('INTER00013464')

trans1_wav = CreateTransmissionWorkspaceAuto(trans1)
trans2_wav = CreateTransmissionWorkspaceAuto(trans2)

wsGroup1 = GroupWorkspaces("trans1_wav")
wsGroup2 = GroupWorkspaces("trans2_wav")

stitched_wav1, y = Stitch1DMany("wsGroup1,wsGroup2", params='1, 0.02, 17', UseManualScaleFactor=True, ManualScaleFactor=0.85)
stitched_wav2, y = Stitch1DMany("wsGroup1,wsGroup2", params='1, 0.05, 17', UseManualScaleFactor=True, ManualScaleFactor=3.85)
```