Specifications may get missing when project directory is manually copied

[soininen]

Specifications/plugin paths may point to non-existent locations after a project has been manually copied from one location to another.

[jkiviluo]

The description is bit unclear. When does this happen? How it could be improved?

[DillonJ]

If I have a project with, say, the RunSpineOpt plugin tool and I manually copy it from one machine to another, it doesn't work as the specification for the RunSpineOpt tool is not found.

[jkiviluo]

This should be improved by highlighting missing program files in the workflow interface.

Maybe there should also be a separation between filename and path - it's the path that's wrong, not the filename. While at it, maybe the 'path' should be 'program root folder' and the 'filenames' (main program and supporting files) would be given as a relative path/filename from the that root folder. Then it would be enough to just update the 'program root folder' after moving the project.

The program root folder could also come from the environment. So, fixing this should also account for environments after copying a project. So, relates to #1499 and #2554