Merge pull request #249 from stoewer/master

EntityWithMetadata: setter checks only root fix
rename of Dimension::id to Dimension::index
fixed tests that involve dimension ids, respectively the index
Merge pull request #250 from jgrewe/dim_index

Renaming of Dimension::id to Dimension::index

Cool, thanks!
Rename pandora in comments and include guards
Rename file format string to nix
Rename pandora in *.md files and CMakeLists.txt