[REG 4.1 -> 4.2] Each pass of project parsing leads to different results

1. Have a checkout of Creator's repository at tag v4.1.0-beta1.
2. In Creator, configure two kits:
   1. The default kit uses Qt 5.3.1.
   2. Another kit uses Qt 5.6.1.
3. Open project qtcreator.pro from the repository.
   You'll get to the "Configure Project" screen. There you can read that Creator uses Qt 5.3.1 for parsing the project.
4. Go to Edit mode.
5. In the Projects view, expand nodes qtcreator/share/static/Sources.
   There is a node "scripts" containing the file openTerminal.command.
6. Go to Projects mode.
7. Only check the kit using Qt 5.3.1 and click "Configure Project".
8. Go to Edit mode.
9. In the Projects view, expand nodes qtcreator/share/static/Sources.
   The node "scripts" has disappeared.
10. Go to Projects mode.
11. Make the kit using Qt 5.6.1 the active kit.
12. Wait for parsing to finish.
13. Make the kit using Qt 5.3.1 the active kit.
14. Go to Edit mode.
15. The Projects view contains the root node only.

Creator parsed the project using Qt 5.3.1 three times and got three different results. Parsing with the same kit should always lead to the same result.
When opening qtcreator.pro from current 4.2 branch, this seems to work correctly.

Found by Squish test tst_openqt_creator.