GEMSHOME removal

[Pshepp]

To help make life easier, we should go ahead and begin removing our reliance or more so unnecessary constraint of utilizing the GEMSHOME variable.

I have begun using patterns that do not rely upon the env var, and began changing up the prepush tests so it does not require the environment variable.

[Pshepp]

Added the bug label because requiring the GEMSHOME env variable in so many places completely boogers up workflows and feels gross so its a bug. Plus we can make life oh so much easier and make the code more stronk. For example, I have removed a ton of the gemshome requirements from GMML to the point that I can just click "commit" on gitkraken and everything runs correctly

Also we even have c++ code dependent on environment variables, we should almost never do this it is mad ugly.

File that is dependent on an environment variable, idk if this file is in use. @gitoliver plz help after your back from vacation :japanese_ogre: : src/MolecularModeling/Assembly/SugarIdentification/oligosaccharidedetection.cc

[Lachele]

Assigning Dave. This is probably stale code. The use of getenv also wants to make an "Ontologies" directory inside of gems. I don't think this has been desirable behavior in a while. Can the use of GEMSHOME just go?

[gitoliver]

That code is still in use by glyfinder and Yao's glycomimetic tool. If you can edit it to not use $GEMSHOME, and still have the tests pass you should be fine. I would ask Yao to run tests separately as his glycomimetic tool isn't integrated.

[Pshepp]

This is mostly a note for myself so I keep tabs on this and know it is current. I want to make some of the replacement logic more robust and bullet proof but am wrapping some other things up rn. Going to also assign to myself so i can keep track of this more easily.