BI-2476 Create Single and Batch Delete End Points for Germplasm

[dmeidlin]

Story: BI-2476

This pull request implements a "soft delete" functionality for germplasm data, meaning that instead of permanently deleting germplasm records, they are marked as deleted. This provides a mechanism for data recovery and avoids data loss. A hard delete option is also implemented. The pull request also fixes a typo in the PedigreeEdgeEntity related to connectedNode.

Key Changes:

Germplasm Deletion Endpoint: Adds a new API endpoint to delete germplasm records. The endpoint supports both hard deletes (permanent deletion) and soft deletes.
Soft Delete Implementation: Introduces a softDeleted boolean field to the GermplasmEntity to indicate whether a record has been soft deleted. The entity is also updated with a @where clause so that only non-deleted entities are returned by default.
Database Migration: Adds SQL migration scripts to add the soft_deleted column to the germplasm table.
Repository Updates: The GermplasmRepository is updated with new methods to perform the soft delete.
Controller Updates: The GermplasmApiController is updated to implement batch deletes.
Typo Fix: Corrects a typo in the PedigreeEdgeEntity class, replacing conncetedNode with connectedNode. This change is reflected in the corresponding database migration and JPQL queries.
Component Factory Updates: Updated the GermplasmComponent to use the correct service methods for batch soft and hard deletes.

The following associated entities will cascade delete when a germplasm record is soft- or hard-deleted:

Germplasm Children

• seed_lot_content_mixture
• reference_set
• observation_unit
• cross_parent
• pedigree_node
• germplasm_taxon
• germplasm_synonym
• germplasm_search_results
• germplasm_origin
• germplasm_institute
• germplasm_entity_type_of_germplasm_storage_code
• germplasm_external_references
• germplasm_attribute_value
• germplasm_donor

Observation Unit Children

• image
• event_observation_units
• observation_unit_treatment
• observation_unit_position
• observation_unit_level
• observation
• observation_unit_external_references

Image Children

• image_observations
• image_external_references
• image_entity_descriptive_ontology_terms

Variant Children

• variant_entity_filters_failed
• variant_entity_cipos
• variant_entity_ciend
• variant_entity_alternate_bases
• variant_external_references

Variant Set Children

• variantset_format
• variantset_external_references
• variantset_analysis

Reference Children

• reference_external_references
• reference_bases

Reference Set Children

• variantset
• variant
• reference
• reference_set_external_references

Pedigree Node Child

• pedigree_edge

Pedigree Edge Child

• pedigree_edge_external_references

Reference Bases Child

• reference_bases_external_references