Refactor/semanticnaming #45
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This branch was made to rename all existing project files to give them more semantic meaning in the file names. The only changes to the code were to make sure import/export statements work.
The selected naming convention uses the following prefixes for files:

"batch" for files explicitly called in the batching process
"log" for files explicitly used in the log generation steps
"oneOff" for files explicitly used in the one off embedding process
"scalar" for files explicitly used in the generation of scalar metrics
"shared" for the one file that is used in both the one off and batched workflow.