In place fixes (rebased onto develop)



This is the same as gh-2648 but rebased onto develop.

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1. print command commit from gh-2242 (See [this thread](https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7542)). To test: try to hard-link across OS boundaries. A better message should be printed than:
```
transfer process returned 1
```