Update doxygen comments and pattern

I have update the doxygen patterns to take into account cpp and hpp files.

I also converted the file names within the doxygen comments to the proper ones.

I proceeded with
```
for ff in `find . -name "*.hpp"` ; do sed -i -r "s/(\w\.h)(\s|\)|\.|$)/\1pp\2/g" $ff ; done
```

and repeated for *.cpp and c extensions instead. Also, a run of
```
sed -i -e 's/elc_params.hpp/elc_params.h/g' elc.cpp
```
corrects a file that gets "extra" corrections due to a ".h" attribute to an object.

I checked manually that only comments were affected.