chore: remove old docs

[PaulNewling]

Greptile Summary

This PR removes two internal documentation files and adds a patch changeset for the root Sequence Properties package.

Important touched terms

• Spec deviation: A documented difference between the authoritative specification and implemented behavior. The PR removes the consolidated deviation log, although current workflow comments and changelogs still reference several of its entries.
• Visualization implementation plan: A temporary design and delivery checklist for the scatterplot and histogram panels. The PR removes it after the corresponding implementation landed.
• Changeset: Release metadata describing which package receives a semantic-version update and why. The PR adds a patch changeset for @platforma-open/milaboratories.sequence-properties.
• SD-001–SD-013: Identifiers for individual implementation deviations, including allele filtering, region normalization, receptor/chain inference, and visualization behavior. Their consolidated definitions and rationale are removed by this PR.

Confidence Score: 4/5

The code behavior is unaffected, but the documentation cleanup should also repair or relocate the remaining references to the deleted deviation log.

The visualization plan is obsolete and the changeset targets a valid package, but deleting the deviation log creates concrete broken references in active workflow comments and changelogs.

Files Needing Attention: docs/spec-deviations.md

Important Files Changed

Filename	Overview
docs/spec-deviations.md	Removes the consolidated record of active implementation deviations while several current code comments and changelogs still link to it.
docs/visualizations-plan.md	Removes an obsolete implementation plan whose core scatterplot and histogram work has already landed.
.changeset/real-llamas-count.md	Adds a valid patch changeset for the published root block package to record the documentation cleanup.

Prompt To Fix All With AI

### Issue 1
docs/spec-deviations.md:1
**Deletion Breaks Active References**

Deleting this deviation log leaves active comments in `workflow/src/main.tpl.tengo` and several package changelogs pointing to a file that no longer exists. Maintainers following those references cannot retrieve the rationale for current behavior such as primary-allele filtering, FR4 normalization, receptor inference, and the deferred visualization reference line. Please preserve or relocate the document, or update all remaining references.

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For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (1): Last reviewed commit: "chore: remove old docs" | Re-trigger Greptile}