Keep Claude Code files local: untrack CLAUDE.md, ignore CLAUDE.md, CLAUDE.local.md and .claude/

.gitignore

@@ -20,3 +20,7 @@ target/
 results/
 # editor lock files
 .~lock.*#
+# Claude Code files (kept local only)
+CLAUDE.md
+CLAUDE.local.md
+.claude/

CLAUDE.md

@@ -1,19 +0,0 @@
-# SimurgArray
-Personal research toolkit for Illumina Infinium genotyping arrays (IDAT→GTC→VCF, QC, CN, PGx).
-The full spec and roadmap is SIMURGARRAY_MASTER_PLAN.md — read the relevant section before changing code.
-Externally visible behaviour (CLI options, file schemas, QC semantics, messages, edge cases) is defined item-by-item
-in SIMURGARRAY_FUNCTIONAL_SPEC.md (IDs like CLI-021, OUT-031); cite item IDs in commits and tests.
-
-## Rules
-- Work phase by phase (§18). Don't start a phase until the previous gate passes.
-- Science modules (signal/, genotype/, cn/, qc/, pgx/) are pure functions; no I/O inside them.
-- Every algorithm cites its source (§7 tags) in its docstring.
-- MIT/BSD/Apache/Unlicense code may be ported with attribution in THIRD_PARTY_NOTICES.md.
-  GPL tools (plink2, illuminaio, verifyIDintensity) = subprocess oracles only; never copy their code.
-- Never commit vendor data (BPM/CSV/EGT/IDAT) — only tests/fixtures/ (Artistic-2.0 Bioconductor files, synthetic data).
-- Never hide oracle discrepancies; record them in docs/known_unknowns.md.
-- Default mode is bit-exact vs Illumina-produced GTCs; keep a clean-math mode too.
-
-## Commands
-- uv sync ; uv run pytest -q ; uv run ruff check . ; uv run mypy src
-- bash scripts/fetch_data.sh p0|p1|p2 ; bash scripts/bootstrap_refs.sh

SIMURGARRAY_MASTER_PLAN.md

@@ -189,7 +189,7 @@ bash scripts/bootstrap_refs.sh && bash scripts/fetch_data.sh p0
 ```
 simurg/
 ├── pyproject.toml            # uv/hatch; package "simurg"; entry point `simurg`
-├── CLAUDE.md                 # Appendix A
+├── CLAUDE.md                 # Appendix A (local only, git-ignored)
 ├── SIMURGARRAY_MASTER_PLAN.md     # this file
 ├── THIRD_PARTY_NOTICES.md
 ├── scripts/