Adapt embedding to DMS data (peptide mode only), SDK update

[mzueva]

Greptile Summary

This PR adds DMS-derived amino-acid sequence support and migrates the repository to the updated Platforma SDK build conventions.

• Sequence selector — identifies compatible input columns under the main axis; now includes pl7.app/sequence columns whose feature is amplicon-sequence and alphabet is aminoacid.
• Amplicon sequence — the synthetic-repertoire-profiler’s whole-variant sequence; now treated as a peptide-family input when constructing embedding scopes.
• Peptide scope — represents a single amino-acid sequence embedded as-is; now receives both peptide and qualifying amplicon-sequence columns.
• Build channel — distinguishes development and release builds; the new scripts set PL_BUILD_CHANNEL explicitly.
• Build variant — controls whether all, binary-only, or no software artifacts are built; scripts now configure this through PL_BUILD_VARIANT.
• Build location — selects local or remote artifact production; scripts now configure this through PL_BUILD_LOCATION.
• Software build — packages declared software artifacts and entrypoints; migrated from pl-pkg build to block-tools software build.
• Updates Platforma SDK and Milaboratories build dependencies, CI script selection, Turbo environment forwarding, structure metadata, formatter exclusions, and release metadata.

Confidence Score: 5/5

The PR appears safe to merge, with the new sequence classification and SDK build migration consistently wired through the checked-in configuration.

The added selector remains restricted to amino-acid sequence columns, its scope mapping matches the intended peptide embedding path, and checked-in CI references resolve to the newly defined build scripts without leaving a concrete broken caller.

Important Files Changed

Filename	Overview
model/src/scopes.ts	Adds a constrained amino-acid amplicon-sequence selector and consistently maps matching entries into the existing peptide scope.
package.json	Replaces legacy root build commands with explicit development, release, location, and artifact-variant scripts used by CI.
turbo.json	Updates build environment declarations for the new SDK build protocol and forwards AWS-related credentials.
software/package.json	Migrates software artifact construction from package-builder to block-tools.
.github/workflows/build.yaml	Configures the reusable workflow to run the new local development and remote release build scripts.
pnpm-workspace.yaml	Advances Platforma SDK and Milaboratories build-tool catalog versions for the build migration.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  A[Candidate columns under main axis] --> B{Sequence selector}
  B -->|feature: peptide<br/>alphabet: aminoacid| C[Peptide scope]
  B -->|feature: amplicon-sequence<br/>alphabet: aminoacid| C
  B -->|VDJ sequence domains| D[Receptor scopes]
  C --> E[Embedding model selection]
  D --> E

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