[codex] Restore allele-count CLI output

[iskandr]

Summary

• route isovar-allele-counts through the dedicated counts dataframe helper
• restore fragment-count columns and the num_*_reads schema promised by the docs
• fix the CLI output description so it matches the command behavior
• add regression coverage for both fragment deduplication and the CLI wiring

Root Cause

isovar-allele-counts was wired to the generic read-evidence dataframe path instead of the dedicated counts helper that already existed in dataframe_helpers.py. That generic path collapses the read lists to lengths but leaves the old ref_reads / alt_reads / other_reads column names and drops fragment counts entirely, so the CLI no longer matched its documented contract.

Validation

• ./lint.sh
• ./test.sh

Closes #164.

[coveralls]

coverage: 93.426% (-0.09%) from 93.511% — codex/fix-allele-counts-cli-output into master

[coveralls]

coverage: 93.426% (-0.09%) from 93.511% — codex/fix-allele-counts-cli-output into master