P1: file parsers, sample sheet, discovery, CLI inspect

Readers for IDAT v3, BPM (locus entries v4-v8), CSV manifest, EGT
(data blocks 5-9) and GTC v3-v5 (plus a layout-preserving GTC writer);
sample-sheet validation (IN-001..IN-014), IDAT discovery and pairing
(IN-020..IN-022), message catalogue and exit codes (CLI-014/016),
JSON Lines logging (CLI-007/008), atomic writes (CLI-011), run manifest,
and `simurg inspect`.

Validation (docs/validation/P1.md): GTC, BPM and EGT readers agree
exactly with Illumina BeadArrayFiles on GSA v4 / GDA v1 files; GTCs
round-trip byte-identically; BPM and CSV manifests are consistent.

tests/unit/test_binutil.py

@@ -0,0 +1,68 @@
+from __future__ import annotations
+
+import gzip
+
+import numpy as np
+import pytest
+from hypothesis import given
+from hypothesis import strategies as st
+
+from simurg.core.errors import FormatError
+from simurg.formats.binutil import BinaryReader, BinaryWriter, load_bytes
+
+
+@given(st.text(max_size=400))
+def test_string_roundtrip(s: str) -> None:
+    w = BinaryWriter()
+    w.string(s)
+    r = BinaryReader(w.getvalue(), "E_GTC_CORRUPT")
+    assert r.string() == s
+    assert r.remaining() == 0
+
+
+@pytest.mark.parametrize("n", [0, 1, 127, 128, 16383, 16384, 300_000])
+def test_varint_boundaries(n: int) -> None:
+    w = BinaryWriter()
+    w.string(b"x" * n)
+    r = BinaryReader(w.getvalue(), "E_GTC_CORRUPT")
+    assert r.varint_length() == n
+
+
+def test_invalid_utf8_is_replaced_not_raised() -> None:  # IN-033, EDGE-002
+    w = BinaryWriter()
+    w.string(b"ok\xff\xfe")
+    assert BinaryReader(w.getvalue(), "E_GTC_CORRUPT").string() == "ok��"
+
+
+def test_string_past_eof_is_format_error() -> None:
+    buf = bytes([50]) + b"short"
+    with pytest.raises(FormatError) as e:
+        BinaryReader(buf, "E_GTC_CORRUPT", "x.gtc").string()
+    assert e.value.code == "E_GTC_CORRUPT"
+
+
+def test_bad_varint_is_format_error() -> None:
+    with pytest.raises(FormatError):
+        BinaryReader(b"\xff\xff\xff\xff\xff\xff", "E_BPM_FORMAT").varint_length()
+
+
+def test_array_bounds_and_seek() -> None:
+    r = BinaryReader(np.arange(4, dtype="<i4").tobytes(), "E_IDAT_FORMAT")
+    assert r.array("<i4", 4).tolist() == [0, 1, 2, 3]
+    r.seek(0)
+    with pytest.raises(FormatError):
+        r.array("<i4", 5)
+    with pytest.raises(FormatError):
+        r.seek(100)
+
+
+def test_load_bytes_gzip(tmp_path) -> None:  # type: ignore[no-untyped-def]
+    p = tmp_path / "a.bin.gz"
+    p.write_bytes(gzip.compress(b"hello"))
+    assert bytes(load_bytes(p)) == b"hello"
+    q = tmp_path / "b.bin"
+    q.write_bytes(b"world")
+    assert bytes(load_bytes(q)) == b"world"
+    e = tmp_path / "empty.bin"
+    e.write_bytes(b"")
+    assert bytes(load_bytes(e)) == b""