Release prep: harden annotation wrapper coverage and CI

[nextgenusfs]

Summary

This PR publishes the completed release-prep work from stress-release-prep into main.

Included commit groups

• 3360044 — test(iprscan): add committed current-namespace XML fixture
• dcca2f2 — fix(tooling): land approved emapper, iprscan, and signalp updates
• deaf45b — ci(release): harden production release workflow and CLI coverage
• ca30d7e — test(antismash): add approved local fixture regression coverage

What changed

• hardens eggNOG-mapper wrapper behavior around stable output prefix / resume-safe output reuse
• fixes current InterProScan XML parsing compatibility and adds committed regression coverage
• adds/extends SignalP and antiSMASH fixture-backed regression coverage
• strengthens CLI coverage and the production release workflow

Verification

Completed before push and recorded in the workspace spec:

• conda run -n f2 python -m pytest tests/unit -v
• focused InterProScan fixture coverage passed in f2
• real InterProScan parse smoke validation passed in f2
• real eggNOG-mapper smoke run passed
• real eggNOG-mapper rerun with --resume passed and reused the stable emapper prefix without creating random-prefix outputs

Notes

• This PR preserves the existing local commit boundaries; no history rewriting was done before push.
• The branch was pushed cleanly from a clean working tree and the remote tip matches local HEAD.

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Pull Request opened by Augment Code with guidance from the PR author