Name the results tables and their columns files after what they hold

[emattei]

Two renames, smallest first.

columns.yaml -> <table>_columns.yaml. A folder that holds one results
table also held a file called columns.yaml, so the name said nothing about
what it documented and two of them could not sit side by side.

The tables themselves. The folder names said which step ran; the file
names did not, and they disagreed on plural. Each table is now singular and
says what the guide was annotated against:

alignments/   guide_genome_annotation.tsv   guide_mapping.bed
              guide_genome_annotation_columns.yaml   qc.tsv
annotations/  guide_gene_annotation.tsv     guide_gene_annotation_columns.yaml
elements/     guide_element_mapping.tsv     guide_element_mapping_columns.yaml   qc.tsv
igvf/         guide_metadata.tsv            guide_metadata_columns.yaml

guide_metadata.tsv keeps its name: it is what the IGVF CRISPR Perturb-seq
pipeline reads, so the name is not ours to change.

This breaks every path a caller has written down, including the
--alignment argument of guide-annotation, element-mapping and
igvf-export. The failure is a clean missing-file error, not silent wrong
behaviour.

The alignment columns file still documents guide_mapping.bed alongside the
tsv, in one document, as it did before.

🤖 Generated with Claude Code