Fix imputeGermline having no effect when assemblingFeature is CDR3

[mzueva]

Greptile Summary

This PR fixes a bug where setting imputeGermline=true had no effect when assemblingFeature was CDR3. The root cause was that parseAssemblingFeature returned an empty imputed list for CDR3 (treating it identically to VDJRegion), so no germline-imputed columns or MiXCR export args were ever produced.

• Core fix (calculate-export-specs.lib.tengo): parseAssemblingFeature now returns [\"FR1\",\"CDR1\",\"FR2\",\"CDR2\",\"FR3\",\"FR4\",\"VDJRegion\"] as the imputed list and [\"CDR3\"] as nonImputed for CDR3 assembly.
• Test file (exportSpecs.test.ts): TypeScript mirror of the Tengo logic with a new test asserting the corrected CDR3 imputed/nonImputed split.
• Dependency & tooling bumps: Routine version upgrades plus adding --registry-serve-url to the publish script.

Confidence Score: 4/5

Safe to merge. The change is targeted and correct: the CDR3 imputed/nonImputed lists are now logically consistent with how CDR3 amplicon sequencing works, and all existing guard conditions remain correct.

The behavioral change to nonImputed for CDR3 means users who ran CDR3 assembly without imputation will no longer see FR1/CDR1/FR2/etc. columns in their output — a silent schema change for existing pipelines. No test exercises the full Tengo runtime for CDR3+imputeGermline=true end-to-end.

workflow/src/calculate-export-specs.lib.tengo carries the core behavioral change and would benefit from an integration-level snapshot test for assemblingFeature=CDR3 with imputeGermline=true.

Important Files Changed

Filename	Overview
workflow/src/calculate-export-specs.lib.tengo	Core bug fix: parseAssemblingFeature now correctly returns imputed: [FR1,CDR1,FR2,CDR2,FR3,FR4,VDJRegion] and nonImputed: [CDR3] for CDR3, enabling germline-imputed columns to be generated.
test/src/exportSpecs.test.ts	TypeScript mirror of the Tengo export-specs logic with new test asserting CDR3 imputed/nonImputed behavior.
.changeset/cdr3-impute-germline.md	Patch-level changeset describing the CDR3 imputation fix accurately.
block/package.json	Adds --registry-serve-url to the prepublishOnly publish command; routine tooling update.
pnpm-workspace.yaml	Catalog version bumps for ts-builder, ts-configs, block-tools, model/test/ui-vue, workflow-tengo, tengo-builder.
pnpm-lock.yaml	Generated lockfile reflecting version bumps; no logic to review.

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