Several of my programs are system tools and therefore have to modify system files.

To my big surprise Nokia now re-reviewed one of those apps and decided to fail it, because it modifies system files.
See below a snipped of the review report:
Comments from the QA team:
The file was re-tested and an issue was discovered:

SUMMARY: The application modifies system files.

1. Install "Rotate Lock Screen" from the Store
2. When installing, copy the debian package of the application safe so it can
be inspected
3. On the device, execute ls -l
4. Take a look at the contents of the debian package:

dpkg-deb --contents rotatelockscreen_1.0.1_armel.deb
ar vx rotatelockscreen_1.0.1_armel.deb
tar zvxf control.tar.gz

5. Take a look at the postinst and prerm scripts:

cat postinst
cat prerm

The application does not modify any Harmattan operating system files.

After step 3, on Harmattan PR1.3, you should see

-rw-r--r-- 1 root root 3418 Mar 1 13:47

In step 5, you should not see scripts modifying Harmattan files.

After step 3, on Harmattan PR1.3, you see

-rw-r--r-- 1 root root 3410 Mar 1 13:47
-rw-r--r-- 1 root root 3418 Mar 1 13:47

(the css file has been modified)

In step 5, you see

sed -i 's/ locked-orientation: "portrait";/ locked-orientation: "";/'
How do I have to proceed?
Instead of failing the app, Nokia should say what I have to change.

As you can see on the links below, the apps are working all fine and almost all users are fine with them. (The ones who are not happy seem either not to understand the function of the app or do not know how to use their phone properly):

This is not the first time Nokia changes their QA rules out of the blue and it is very frustrating!!!
This way, developers really are dis-encouraged to invest into Harmattan.