Replace last references to counted_ptr

Some parts of the code still relied on counted_ptr which was removed in eudaq/eudaq#39 and replaced by std::shared_ptr -- this PR fixes this and thus fixes issue eudaq/eudaq#47

This is basically the result of
```
for i in `grep counted_ptr * -rIl`; do sed 's/^.*include.*counted_ptr.*$//g' $i > $i.new; mv $i.new $i; done
for i in `grep counted_ptr * -rIl`; do sed 's/counted_ptr/std::shared_ptr/g' $i > $i.new; mv $i.new $i; done
```
and was tested on Ubuntu 12.10, gcc 4.7, CMake 2.8.12

Also fixes an issue with CMake scripts for ZestSC1 on Linux.