Make reordering and reindexing of entries optional when saving database

[davidfarinajr]

Motivation or Problem

When loading and saving the database, the entries are automatically re-ordered and re-indexed using the get_entries_to_save function. While it is nice to have this option, sometimes we do not want to reorder and reindex when adding new entries because the entire file may be rewritten in the git commit history.

Description of Changes

This PR makes the reordering and reindexing optional when saving.

Testing

I used this branch when saving the thermo groups in PR https://github.com/ReactionMechanismGenerator/RMG-database/pull/414.