docs(tri): Integrate scientific writing methodology into /tri system

Integrate IMRaD structure and reproducibility best practices into T27
autonomous agent system. This enables agents to generate academic papers following
scientific writing standards and ensure research is reproducible.

Добавление научной методологии написания в систему /tri.

Интеграция структуры IMRaD и лучших практик воспроизводимости в автономную
систему агента T27. Это позволяет агентам генерировать академические работы,
следуя научным стандартам письма, и обеспечивать воспроизводимость исследований.

Files:
- specs/tri/scientific_writing.tri - Scientific writing system with IMRaD structure
- specs/tri/reproducibility.tri - Reproducibility verification and scoring
- src/tri/cells/science/cell.tri - Updated with scientific capabilities
- docs/scientific/ - Directory for generated papers

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: Dmitrii Vasilev

specs/tri/reproducibility.tri

@@ -0,0 +1,260 @@
+# ═══════════════════════════════════════════════════════════════════════════════
+# VIBEE Specification — Scientific Reproducibility System
+# ═══════════════════════════════════════════════════════════════════════════════
+# Code + Data + Environment = Reproducible Science
+# ═════════════════════════════════════════════════════════════════════════════════
+
+name: reproducibility
+version: "1.0.0"
+language: zig
+module: reproducibility
+
+description: |
+  Scientific Reproducibility System verifies and ensures research can be replicated.
+  Checks code availability, environment documentation, data provenance, and metadata.
+  Generates reproducibility scores and reports missing elements.
+
+types:
+  ReproducibilityItem:
+    fields:
+      name: String
+      description: String
+      present: Bool
+      required: Bool
+      path: String
+
+  EnvironmentInfo:
+    fields:
+      has_dockerfile: Bool
+      dockerfile_path: String
+      image_tag: String
+      base_image: String
+      compiler_versions: List<String>
+      dependency_versions: List<String>
+
+  DataProvenance:
+    fields:
+      datasets_versioned: Bool
+      semantic_versioning: Bool
+      repository_urls: List<String>
+      doi_available: Bool
+      hash_checksums: Bool
+      raw_data_preserved: Bool
+
+  DocumentationStatus:
+    fields:
+      has_readme: Bool
+      has_api_docs: Bool
+      has_setup_guide: Bool
+      has_experiment_examples: Bool
+      has_metadata_docs: Bool
+
+  ReproducibilityReport:
+    fields:
+      overall_score: Float
+      code_available: Bool
+      environment_ok: Bool
+      data_tracked: Bool
+      documentation_complete: Bool
+      missing_items: List<String>
+      recommendations: List<String>
+
+  ReproducibilityConfig:
+    fields:
+      project_path: String
+      strict_mode: Bool
+      threshold_score: Float
+      check_code: Bool
+      check_environment: Bool
+      check_data: Bool
+      check_docs: Bool
+
+constants:
+  DEFAULT_THRESHOLD: Float = 0.8
+  PERFECT_SCORE: Float = 1.0
+  MINIMUM_ACCEPTABLE: Float = 0.6
+  CODE_WEIGHT: Float = 0.3
+  ENVIRONMENT_WEIGHT: Float = 0.25
+  DATA_WEIGHT: Float = 0.25
+  DOCUMENTATION_WEIGHT: Float = 0.2
+
+behaviors:
+  - name: checkReproducibility
+    given: config: ReproducibilityConfig
+    when: User runs `tri repro_check <project>`
+    then: Analyze project and return ReproducibilityReport
+    test_cases:
+      - name: test_perfect_reproducibility
+        input: "{\"mock_complete\": true}"
+        expected: "{\"score\": 1.0}"
+      - name: test_missing_docker
+        input: "{\"has_dockerfile\": false}"
+        expected: "{\"environment_ok\": false}"
+
+  - name: checkCodeAvailability
+    given: project_path: String
+    when: Verifying code is in open repository
+    then: Return boolean + repository URL
+    test_cases:
+      - name: test_public_repo
+        input: "{\"is_public\": true}"
+        expected: "{\"available\": true}"
+
+  - name: checkEnvironmentSetup
+    given: project_path: String
+    when: Checking Docker/container environment
+    then: Return EnvironmentInfo with Dockerfile status
+    test_cases:
+      - name: test_dockerfile_exists
+        input: "{\"has_dockerfile\": true}"
+        expected: "{\"has_dockerfile\": true}"
+
+  - name: checkDataProvenance
+    given: project_path: String
+    when: Verifying data versioning and tracking
+    then: Return DataProvenance status
+    test_cases:
+      - name: test_versioned_data
+        input: "{\"versioned\": true}"
+        expected: "{\"datasets_versioned\": true}"
+
+  - name: checkDocumentation
+    given: project_path: String
+    when: Assessing documentation completeness
+    then: Return DocumentationStatus
+    test_cases:
+      - name: test_complete_docs
+        input: "{\"has_all\": true}"
+        expected: "{\"complete\": true}"
+
+  - name: calculateReproducibilityScore
+    given: code_ok: Bool, env_ok: Bool, data_ok: Bool, docs_ok: Bool
+    when: Computing overall score
+    then: Return weighted score 0.0-1.0
+    test_cases:
+      - name: test_all_true
+        input: "{\"all\": true}"
+        expected: "{\"score\": 1.0}"
+      - name: test_partial
+        input: "{\"code\": true, \"env\": true, \"data\": false, \"docs\": true}"
+        expected: "{\"score\": 0.75}"
+
+  - name: generateRecommendations
+    given: report: ReproducibilityReport
+    when: Creating improvement suggestions
+    then: Return list of actionable recommendations
+    test_cases:
+      - name: test_docker_recommendation
+        input: "{\"missing\": [\"dockerfile\"]}"
+        expected: "{\"recommendations\": [\"Create Dockerfile\"]}"
+
+  - name: validateDockerfile
+    given: dockerfile_path: String
+    when: Checking Dockerfile quality
+    then: Return validation with pinned versions check
+    test_cases:
+      - name: test_pinned_versions
+        input: "{\"uses_latest\": false}"
+        expected: "{\"valid\": true}"
+
+  - name: checkTestVectors
+    given: project_path: String
+    when: Verifying test vectors exist
+    then: Return boolean + count of test vectors
+    test_cases:
+      - name: test_vectors_present
+        input: "{\"count\": 10}"
+        expected: "{\"available\": true}"
+
+  - name: generateMetadataReport
+    given: project_path: String
+    when: Creating metadata completeness report
+    then: Return report with parameter tracking status
+    test_cases:
+      - name: test_full_metadata
+        input: "{\"has_params\": true}"
+        expected: "{\"complete\": true}"
+
+  - name: exportReproducibilityBadge
+    given: score: Float
+    when: Generating badge for README
+    then: Return SVG badge with score color
+    test_cases:
+      - name: test_green_badge
+        input: "{\"score\": 0.9}"
+        expected: "{\"color\": \"green\"}"
+
+integration:
+  std.fs:
+    module: std.fs
+    functions:
+      - cwd
+      - openFile
+      - access
+
+  std.mem:
+    module: std.mem
+    functions:
+      - Allocator
+
+  tri_context:
+    module: tri_context
+    functions:
+      - getProjectPath
+
+  github_commands:
+    module: github_commands
+    functions:
+      - checkRepoVisibility
+
+  tri_commands:
+    module: tri_commands
+    functions:
+      - runChatCommand
+
+# ═══════════════════════════════════════════════════════════════════════════════
+# IMPLEMENTATION NOTES
+# ═══════════════════════════════════════════════════════════════════════════════
+#
+# 1. Reproducibility Score Calculation:
+#    score = (code_ok * 0.3) + (env_ok * 0.25) + (data_ok * 0.25) + (docs_ok * 0.2)
+#    Threshold: 0.8 for "reproducible" status
+#
+# 2. Code Availability Check:
+#    - Repository is public (GitHub/GitLab)
+#    - Has proper LICENSE file
+#    - Version control (git tags/releases)
+#
+# 3. Environment Setup:
+#    - Dockerfile exists and uses pinned versions (not :latest)
+#    - Base image is stable (Ubuntu LTS, debian:stable)
+#    - Compiler versions specified
+#    - Dependency versions locked
+#
+# 4. Data Provenance:
+#    - Datasets versioned (v1.0.0, v1.1.0, ...)
+#    - Raw data preserved
+#    - Checksums/hashes available
+#    - DOI for datasets (Zenodo, Figshare)
+#    - Repository URLs documented
+#
+# 5. Documentation:
+#    - README with setup instructions
+#    - API documentation
+#    - Example experiments
+#    - Parameter metadata
+#
+# 6. CLI Command: `tri repro_check <project_path>`
+#    - Outputs: Score breakdown, missing items, recommendations
+#    - Exit code: 0 if score >= threshold, 1 otherwise
+#    - Flag: --strict fails on any missing item
+#
+# 7. Badge Generation:
+#    - Score >= 0.9: green (Excellent)
+#    - Score >= 0.8: yellow (Good)
+#    - Score >= 0.6: orange (Fair)
+#    - Score < 0.6: red (Needs improvement)
+#
+# ═════════════════════════════════════════════════════════════════════════════════
+# END OF SPECIFICATION
+# ═════════════════════════════════════════════════════════════════════════════════════════════