Incorrect indexes

There's an index attribute for all entries in training reactions, kinetics groups & libraries, and thermo groups and libraries. The original purpose was just for referencing: its easier to point somebody to index number 60 than to a possibly long string title. Additionally, these indexes originally matched up with the order in Java.

Currently, we know that there it no longer matches Java, and there are accidental duplicates. It is also an inconvenience to pick an non-duplicate and non-arbitrary index when adding new entries. It seems like there are two options to clean these up:

1. Eliminate the attribute altogether. I have personally never used an index number to reference it to another person, and there's an argument that the string label is easy enough to copy and paste.
2. Write a script to clean up indexes in the files. If we do this, we can maintain the original function, but it would be a nice feature to put the largest index on the top of every file.

I'm okay with either of these options. How do other people feel about this?

First inspect the index attributes in the training reactions, kinetics groups and libraries, and thermo groups and libraries files. Resolve whether the project wants to remove the attributes or clean them with a script; done means the chosen approach eliminates accidental duplicates and no longer requires arbitrary indexes.