Remove annotations as preprocessing for various CIF tools

See #735 (closed) for adding the CIF to CIF transformation to remove annotations. It could be added to various CIF tools, that don't process annotations, and can support more specifications by removing annotations as preprocessing. Should be carefully considered for tools that also output CIF specifications, and then removing them may not be the best option.

• Do it for all tools, except for CIF controller checker. (!900 (merged))
• Do it for CIF controller checker. (!901 (merged))

Addresses #593 (closed)