Establish BlackSTAR as an independent STAR successor

[justinblethrow-cloud]

Summary

This change establishes BlackSTAR as an explicitly independent, community-maintained
successor to STAR while preserving clear lineage, attribution, and compatibility
boundaries.

• defines independent project identity, governance, support, security, and contribution policies
• separates BlackSTAR release versioning from STAR compatibility and genome-format versions
• adds --version-json for machine-readable deployment and provenance checks
• documents migration, compatibility, release policy, measured performance, and the 1.0.0 scope
• adds pinned CI, compiler-matrix, CodeQL, reproducible-release, SBOM, and artifact-attestation workflows
• adds issue/PR templates and declarative post-detachment repository settings
• adds recovery-tested GitHub transition tooling with explicit guards around permanent detachment
• expands the architecture atlas with successor, compatibility, and governance diagrams

The transition does not change alignment or index algorithms relative to the released
2.7.11b-blackstar.2 code. It promotes that qualified implementation into an
independently versioned project and adds release/governance infrastructure.

Compatibility identity

• BlackSTAR release: 1.0.0
• executable lineage: 2.7.11b-blackstar.3
• STAR compatibility baseline: 2.7.11b
• genome index format: 2.7.4a
• legacy --version remains wrapper-compatible
• new --version-json exposes all four identities explicitly

Evidence

The committed benchmark evidence compares official STAR 2.7.11b with released
BlackSTAR .2 under paired, order-balanced trials:

• CHM13 full index generation: 1256.03 s to 607.18 s median, 51.44% lower wall time
• 96-thread uncompressed alignment: 82.49 s to 55.20 s, 33.11% lower wall time
• 96-thread gzip-input alignment: 90.22 s to 63.15 s, 30.75% median paired reduction
• cold Delta update: 1225.62 s full rebuild to 39.04 s, 31.50x faster

Correctness evidence includes index equivalence, mapping equivalence, Delta equivalence,
and GFP/GST insertion tests. Exact methods, trial values, resource tradeoffs, and scope
limitations are committed under docs/benchmarks/ and docs/PERFORMANCE.md.

Local qualification of commit 87f235544d90a9f9bd4220a86eef6bc0f713e0b2 passed:

• clean reproducible release build with OpenMP linkage, legal files, SPDX SBOM, and provenance
• release archive SHA-256: 7012c09b98957a02a14ca440aa01e695456d43f2219ba5809bc2e38a330201dd
• successor metadata, version, architecture provenance, benchmark-harness, and deployment-selector gates
• 8 focused sanitizer/unit scripts
• 24 genome-insert hardening checks against an official STAR 2.7.11b oracle
• 4 SAindex strategy-equivalence checks
• two independently built release packages were byte-identical

GitHub CI is the authoritative clean-environment gate for this PR, including both GCC
and Clang builds, complete acceptance tests, architecture source reproducibility, and
CodeQL analysis.

Transition boundary

This PR does not:

• detach the repository from the upstream GitHub fork network
• rename or modify the protected default branch
• create the v1.0.0 tag or release
• change any Plasmidsaurus production integration

After CI passes, a final independently verified recovery archive and detachment-readiness
receipt will be created. Permanent fork-network detachment remains a separate,
explicitly approved operation.

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