docs: establish reproducibility provenance contract

Create the public OTTER reproducibility dataset with its data card and per-file provenance schema. Fixture payloads will follow checksum and source validation.

README.md

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+---
+license: mit
+pretty_name: OTTER reproducibility data
+---
+
+# OTTER reproducibility data
+
+This public dataset contains versioned, real-data fixtures and provenance records used to reproduce the executable validation claims for **OTTER** (Orchestrated Transcriptomic, Tumor-xenograft, and Epigenomic Reporting Workflow).
+
+## Scope
+
+The dataset will contain compact, deterministic derivatives of accessioned sequencing data; BAM/BAI fixtures; expected outputs; Gate A–D oracles; RNA-PDX and BS-PDX mixture inputs; and Xenofilx parameter-sweep measurements. It does not contain manuscript materials, private Slurm controllers, full-scale production runs, or full reference-genome snapshots.
+
+GitHub Actions consume this dataset for fixture-based checks only. They do not run full FASTQ mapping/alignment. Normal CI reference acquisition uses official upstream FASTA/GTF sources and pinned reference contracts. The separate [`fallingstar10/xdxtools-genomes`](https://huggingface.co/datasets/fallingstar10/xdxtools-genomes) dataset is the offline reference snapshot and is updated only after CI validation.
+
+## Initial publication status
+
+This initial revision establishes the public repository and the machine-readable provenance contract. Fixture files will be added only after their original accession, Paracloud source path, deterministic derivation method, size, SHA-256, and intended validation scope have been independently verified. No unreviewed legacy manifest or path-bearing log is included in this revision.
+
+## Planned layout
+
+```text
+provenance/
+  schema.json
+  files.jsonl
+  checksums.sha256
+fastqcx/
+bamdriver/gate-a/
+pairbam/gate-b/
+xenofilx/rna-pdx/{gate-c,gate-d,mixing,parameter-sweep}/
+xenofilx/bs-pdx/{gate-c,gate-d,mixing,parameter-sweep}/
+methx/
+qctb/
+seq2mat/
+matsrun/
+enva/
+craftmake/
+otter/
+```
+
+Each line in `provenance/files.jsonl` conforms to `provenance/schema.json`. The required `owner` object identifies the repository, workflow, validation gate, and assay. The required `derivation` object records the SRA accession, Paracloud source path, method, seed when applicable, and input/output counts.
+
+## Validation policy
+
+- All supplied files are checksum-verified before use.
+- RNA-PDX and BS-PDX evidence is independently scoped.
+- Xenofilx parameter recommendations apply only to the documented assay and fixture.
+- Results and logs from scientific CI are published as GitHub Actions artifacts, including failure cases.
+- Full raw-read mapping, manuscript-scale benchmarking, and private Paracloud operations are outside GitHub-hosted CI.
+
+## Citation
+
+Use the future OTTER software release tag together with the exact Hugging Face dataset revision SHA shown by the workflow or provenance record.

provenance/schema.json

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+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://huggingface.co/datasets/fallingstar10/otter-data/resolve/main/provenance/schema.json",
+  "title": "OTTER reproducibility file provenance",
+  "description": "One JSON object per file in provenance/files.jsonl.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "schema_version",
+    "dataset_revision",
+    "dataset_path",
+    "file_role",
+    "file_format",
+    "owner",
+    "derivation",
+    "counts",
+    "source_commit",
+    "size_bytes",
+    "sha256",
+    "created_at_utc"
+  ],
+  "properties": {
+    "schema_version": {
+      "const": "otter.provenance.file/v1"
+    },
+    "dataset_revision": {
+      "type": "string",
+      "minLength": 1
+    },
+    "dataset_path": {
+      "type": "string",
+      "pattern": "^[^/].*"
+    },
+    "file_role": {
+      "enum": [
+        "fixture",
+        "oracle",
+        "expected_output",
+        "metric",
+        "log",
+        "reference_contract",
+        "parameter_grid",
+        "recommendation"
+      ]
+    },
+    "file_format": {
+      "type": "string",
+      "minLength": 1
+    },
+    "owner": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["repository", "workflow", "gate", "assay"],
+      "properties": {
+        "repository": { "type": "string" },
+        "workflow": { "type": "string" },
+        "gate": { "type": "string" },
+        "assay": { "type": "string" }
+      }
+    },
+    "derivation": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["sra_accession", "paracloud_source_path", "method"],
+      "properties": {
+        "sra_accession": { "type": "string" },
+        "paracloud_source_path": { "type": "string" },
+        "method": { "type": "string" },
+        "random_seed": { "type": ["string", "null"] }
+      }
+    },
+    "counts": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["unit", "input", "output"],
+      "properties": {
+        "unit": { "enum": ["reads", "pairs", "templates", "records", "files"] },
+        "input": { "type": ["integer", "null"], "minimum": 0 },
+        "output": { "type": ["integer", "null"], "minimum": 0 }
+      }
+    },
+    "source_commit": {
+      "type": "string",
+      "minLength": 7
+    },
+    "size_bytes": {
+      "type": "integer",
+      "minimum": 0
+    },
+    "sha256": {
+      "type": "string",
+      "pattern": "^[a-f0-9]{64}$"
+    },
+    "created_at_utc": {
+      "type": "string",
+      "format": "date-time"
+    },
+    "notes": {
+      "type": "string"
+    }
+  }
+}