SimurgArray: master plan, repo scaffolding and data/ref fetch scripts

Phase 0 deliverables: full technical specification and roadmap
(SIMURGARRAY_MASTER_PLAN.md), CLAUDE.md, bootstrap script for reference
open-source repos and tiered dataset fetch script with checksums.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

scripts/bootstrap_refs.sh

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+# Shallow-clone reference open-source repositories into refs/ (git-ignored).
+# GPL repos are for use as external oracles only — do not copy their code into SimurgArray.
+set -euo pipefail
+cd "$(dirname "$0")/.."
+mkdir -p refs
+repos=(
+  "Illumina/BeadArrayFiles"        # BSD-2
+  "Illumina/GTCtoVCF"              # Apache-2.0
+  "freeseek/gtc2vcf"               # MIT
+  "freeseek/mocha"                 # MIT
+  "broadinstitute/picard"          # MIT (see src/main/java/picard/arrays)
+  "WGLab/PennCNV"                  # Unlicense
+  "sbslee/pypgx"                   # MIT
+  "PharmGKB/PharmCAT"              # MPL-2.0 (oracle)
+  "HenrikBengtsson/illuminaio"     # GPL-2 (oracle only)
+  "gjun/verifyIDintensity"         # GPL-3 (oracle only)
+)
+for r in "${repos[@]}"; do
+  d="refs/${r#*/}"
+  if [[ -d "$d/.git" ]]; then echo "skip $d"; continue; fi
+  git clone --depth 1 "https://github.com/$r.git" "$d"
+done
+echo "done: $(ls refs | wc -l) repos in refs/"