Establish BlackSTAR as an independent STAR successor

.github/CODEOWNERS

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+* @justinblethrow-cloud
+
+/source/ @justinblethrow-cloud
+/extras/tests/ @justinblethrow-cloud
+/extras/scripts/buildBlackSTARRelease.sh @justinblethrow-cloud
+/.github/ @justinblethrow-cloud
+/SECURITY.md @justinblethrow-cloud
+/GOVERNANCE.md @justinblethrow-cloud

.github/ISSUE_TEMPLATE/bug-report.yml

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+name: Bug report
+description: Report reproducible incorrect behavior or a crash
+title: "[Bug]: "
+labels:
+  - "type: bug"
+  - "needs: triage"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Do not include private sequence data, customer identifiers, credentials, or presigned URLs.
+  - type: input
+    id: version
+    attributes:
+      label: BlackSTAR version
+      description: Paste `STAR --version` and the executable SHA-256.
+    validations:
+      required: true
+  - type: textarea
+    id: command
+    attributes:
+      label: Command and environment
+      description: Include the complete command and relevant environment variables.
+      render: shell
+    validations:
+      required: true
+  - type: textarea
+    id: behavior
+    attributes:
+      label: Observed and expected behavior
+    validations:
+      required: true
+  - type: textarea
+    id: reproducer
+    attributes:
+      label: Minimal reproducer
+      description: Provide synthetic or public inputs and exact reproduction steps.
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Logs
+      description: Attach or paste relevant sections of `Log.out` and `Log.final.out`.
+    validations:
+      required: true
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: OS, CPU, RAM, filesystem, storage placement, compiler or package source.
+    validations:
+      required: true
+  - type: dropdown
+    id: upstream
+    attributes:
+      label: Official STAR 2.7.11b comparison
+      options:
+        - "Official STAR does not reproduce the behavior"
+        - "Official STAR reproduces the behavior"
+        - "Not yet tested"
+        - "Not applicable to a BlackSTAR-only feature"
+    validations:
+      required: true
+  - type: checkboxes
+    id: confirmation
+    attributes:
+      label: Data safety
+      options:
+        - label: I removed private data, credentials, and customer information.
+          required: true

.github/ISSUE_TEMPLATE/compatibility-report.yml

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+name: Compatibility report
+description: Report a STAR interface, index, output, or wrapper incompatibility
+title: "[Compatibility]: "
+labels:
+  - "type: compatibility"
+  - "needs: triage"
+body:
+  - type: dropdown
+    id: surface
+    attributes:
+      label: Compatibility surface
+      options:
+        - Command-line interface
+        - Conventional genome index
+        - Alignment output
+        - Shared-memory lifecycle
+        - Wrapper or workflow integration
+        - Overlay or Delta package
+        - Other
+    validations:
+      required: true
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions and identities
+      description: BlackSTAR, official STAR, wrapper, index, and executable identities.
+    validations:
+      required: true
+  - type: textarea
+    id: reproducer
+    attributes:
+      label: Minimal reproducer and observed difference
+    validations:
+      required: true
+  - type: textarea
+    id: contract
+    attributes:
+      label: Expected compatibility
+      description: Link the relevant compatibility promise or explain the expected inherited behavior.
+    validations:
+      required: true
+  - type: checkboxes
+    id: confirmation
+    attributes:
+      label: Data safety
+      options:
+        - label: I removed private data, credentials, and customer information.
+          required: true

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: BlackSTAR questions and design discussion
+    url: https://github.com/justinblethrow-cloud/blackSTAR/discussions
+    about: Use Discussions for questions that are not reproducible defects.
+  - name: Private security report
+    url: https://github.com/justinblethrow-cloud/blackSTAR/security/advisories/new
+    about: Report suspected vulnerabilities privately.

.github/ISSUE_TEMPLATE/feature-request.yml

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+name: Feature request
+description: Propose a broadly useful BlackSTAR capability
+title: "[Feature]: "
+labels:
+  - "type: enhancement"
+  - "needs: triage"
+body:
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem
+      description: Describe the user or operational problem independently of a proposed implementation.
+    validations:
+      required: true
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed behavior
+    validations:
+      required: true
+  - type: textarea
+    id: compatibility
+    attributes:
+      label: Compatibility and correctness impact
+      description: Explain affected CLI, index, output, resource, or lifecycle contracts.
+    validations:
+      required: true
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+    validations:
+      required: true
+  - type: textarea
+    id: validation
+    attributes:
+      label: Proposed validation
+      description: State how biological correctness, determinism, and practical value would be established.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/performance-regression.yml

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+name: Performance regression
+description: Report a reproducible slowdown or resource regression
+title: "[Performance]: "
+labels:
+  - "type: performance"
+  - "needs: triage"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Performance reports require a matched control and correctness checks. Absolute timings from unrelated systems are not sufficient.
+  - type: input
+    id: candidate
+    attributes:
+      label: Candidate identity
+      description: BlackSTAR version, commit, build flags, and executable SHA-256.
+    validations:
+      required: true
+  - type: input
+    id: control
+    attributes:
+      label: Control identity
+      description: Pinned BlackSTAR or official STAR version and executable SHA-256.
+    validations:
+      required: true
+  - type: textarea
+    id: workload
+    attributes:
+      label: Workload
+      description: Inputs, index, read count and length, output mode, thread count, and commands.
+    validations:
+      required: true
+  - type: textarea
+    id: system
+    attributes:
+      label: System and cache state
+      description: CPU topology, RAM, NUMA policy, filesystem, storage device, competing load, and cold/warm definition.
+    validations:
+      required: true
+  - type: textarea
+    id: measurements
+    attributes:
+      label: Measurements
+      description: Order-balanced replicates, wall time, CPU use, peak RSS, and variability.
+    validations:
+      required: true
+  - type: textarea
+    id: correctness
+    attributes:
+      label: Correctness comparison
+      description: Metrics, junctions, counts, BAM canonicalization, index identity, or other applicable gates.
+    validations:
+      required: true
+  - type: checkboxes
+    id: confirmation
+    attributes:
+      label: Confirmation
+      options:
+        - label: Candidate and control used identical inputs and resource allocation.
+          required: true
+        - label: I removed private data, credentials, and customer information.
+          required: true

.github/PULL_REQUEST_TEMPLATE.md

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+## Purpose
+
+Describe the user-visible change and why it belongs in BlackSTAR.
+
+## Origin Classification
+
+- [ ] Inherited upstream behavior or fix
+- [ ] BlackSTAR regression fix
+- [ ] BlackSTAR-specific feature
+- [ ] Documentation, test, or maintenance only
+
+## Compatibility and Risk
+
+Describe CLI, index, output, resource, concurrency, and lifecycle effects.
+
+## Validation
+
+List exact commands, tests, sanitizers, fixtures, and output comparisons.
+
+## Performance Evidence
+
+For a performance claim, identify the pinned control and candidate, matched
+workload, order-balanced replicates, system/cache state, wall time, CPU, peak
+RSS, variability, and correctness gates. Write `Not applicable` otherwise.
+
+## Documentation
+
+- [ ] Tests would fail without the change
+- [ ] User-facing behavior and changelog are updated
+- [ ] Generated architecture artifacts are synchronized
+- [ ] No private data, credentials, or customer information is included

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    open-pull-requests-limit: 5
+    labels:
+      - "type: dependencies"
+  - package-ecosystem: npm
+    directory: /extras/docs
+    schedule:
+      interval: monthly
+    open-pull-requests-limit: 5
+    labels:
+      - "type: dependencies"

.github/repository-settings.json

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+{
+  "schema_version": 1,
+  "repository": {
+    "default_branch": "main",
+    "description": "Independently maintained, performance-oriented successor to the STAR RNA-seq aligner",
+    "homepage": "https://justinblethrow-cloud.github.io/blackSTAR/",
+    "features": {
+      "discussions": true,
+      "issues": true,
+      "wiki": false
+    },
+    "private_vulnerability_reporting": true,
+    "topics": [
+      "bioinformatics",
+      "genomics",
+      "high-performance-computing",
+      "openmp",
+      "rna-seq",
+      "star-aligner",
+      "transcriptomics"
+    ]
+  },
+  "pages": {
+    "branch": "gh-pages",
+    "path": "/"
+  },
+  "branch_protection": {
+    "allow_deletions": false,
+    "allow_force_pushes": false,
+    "allow_fork_syncing": false,
+    "block_creations": false,
+    "enforce_admins": true,
+    "lock_branch": false,
+    "required_conversation_resolution": true,
+    "required_linear_history": true,
+    "required_pull_request_reviews": {
+      "dismiss_stale_reviews": false,
+      "require_code_owner_reviews": false,
+      "require_last_push_approval": false,
+      "required_approving_review_count": 0
+    },
+    "required_status_checks": {
+      "contexts": [
+        "build-and-test"
+      ],
+      "strict": true
+    },
+    "restrictions": null
+  },
+  "labels": {
+    "needs: reproducer": {
+      "color": "fbca04",
+      "description": "Requires a minimal public reproducer"
+    },
+    "needs: triage": {
+      "color": "d4c5f9",
+      "description": "Requires initial maintainer classification"
+    },
+    "origin: blackstar": {
+      "color": "1d76db",
+      "description": "Behavior introduced by BlackSTAR"
+    },
+    "origin: upstream": {
+      "color": "c5def5",
+      "description": "Behavior inherited from official STAR"
+    },
+    "security": {
+      "color": "b60205",
+      "description": "Security-related work; no private details"
+    },
+    "type: bug": {
+      "color": "d73a4a",
+      "description": "Reproducible incorrect behavior"
+    },
+    "type: compatibility": {
+      "color": "5319e7",
+      "description": "Compatibility contract or integration"
+    },
+    "type: dependencies": {
+      "color": "0366d6",
+      "description": "Dependency maintenance"
+    },
+    "type: enhancement": {
+      "color": "a2eeef",
+      "description": "Proposed feature or improvement"
+    },
+    "type: performance": {
+      "color": "f9d0c4",
+      "description": "Performance or resource behavior"
+    }
+  }
+}