fix the deprecates outs in dvc.lock files when they don't have a match in dvc.yaml files for each repo

[zmughal]

• https://github.com/biobricks-ai/biogrid/pull/1
• https://github.com/biobricks-ai/chebirdf/pull/2
• https://github.com/biobricks-ai/rtecs/pull/1
• https://github.com/biobricks-ai/cpcat/pull/1
• https://github.com/biobricks-ai/toxvaldb/pull/1
• https://github.com/biobricks-ai/cancerharmony/pull/1
• https://github.com/biobricks-ai/cpdat/pull/1
• https://github.com/biobricks-ai/dbgap/pull/1
• https://github.com/biobricks-ai/pdb/pull/2
• https://github.com/biobricks-ai/chembl/pull/6
• https://github.com/biobricks-ai/toxcast/pull/2
• https://github.com/biobricks-ai/moleculenet/pull/1
• https://github.com/biobricks-ai/chebi/pull/1
• https://github.com/biobricks-ai/zinc/pull/1
• https://github.com/biobricks-ai/uniprot-kg/pull/1
• https://github.com/biobricks-ai/USPTO_ChemReaction/pull/1
• https://github.com/biobricks-ai/openfda/pull/1
• https://github.com/biobricks-ai/mesh-kg/pull/1
• https://github.com/biobricks-ai/geneontology/pull/2
• https://github.com/biobricks-ai/qm9/pull/1
• https://github.com/biobricks-ai/pubchem/pull/5

[zmughal]

This is done. The above change to brick-template would be useful to prevent the cause of most of the old stages.