Refactoring Shepherd for testing and maintainability

[vkirkl]

This is a multi-issue story with the goal of breaking the Shepherd class into sub-packages and new classes to facilitate testing and improve maintainability. This iteration will identify and migrate only high priority methods and provide an example for further refactoring as resources allow.
[Sub-issues will be linked as they are created.]

High level tasks include:

1. Enumerate backwards dependencies of Shepherd, ShepherdPMF, and ShepherdProperties; mark orphaned code for removal;
2. Create new directory structure / subpackages
   Suggested directory structure with example files:

   src/main/java/org/ecocean/shepherd/
        core/
            Shepherd.java (Coordinates operations between services and utilities)
            ShepherdPMF.java (Persistence Manager Factory, if not separated out)
        services/
            EncounterService.java
            MediaAssetService.java
            ... 
       utils/
            MediaUtils.java
            QueryUtils.java
            ValidationUtils.java
            ... 
     ```
   

3. Migrate Shepherd and ShepherdPMF to core
4. Identify util methods in Shepherd and prioritize for migration to new util classes based on usage in backwards dependency analysis; migrate high priority methods; add tests; prune code flagged for removal
5. Identify entities and their CRUD methods in Shepherd and prioritize for migration to new service classes; migrate high priority entities (e.g. Encounter); add tests; prune code flagged for removal
6. Identify transaction handling methods; add tests