Fix filename inconsistency

[tracelail]

Fixes #719 — removes double-underscore in output filenames for contrasts without a blocking variable and implements a canonical separator before the method name to . for output files.
Fix 1 — updated CSVTK_JOIN prefix separator from _ to . in conf/modules.config to match the existing ..results.tsv convention from DESEQ2/LIMMA/DREAM modules.
Fix 2 — updated contrast id construction in workflows/differentialabundance.nf with two changes: filtered empty/null values using .findAll before joining to prevent trailing underscores in auto-generated ids, and added a .replaceAll(/_+$/, '') after the if block to catch explicitly set contrast ids that end with a trailing underscore (as seen in the test data).

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir ).
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.