fix: CMYK image drop, empty-doc crash, page_index shadowing, sqlite hardening, flaky tests

Addresses items 9-13 and a/b/c/f from the max-effort review of PR #272.

- pdf.py: image colorspace check was `pix.n > 4`, which treats CMYK-without-
  alpha (n==4, same as RGBA) as not needing RGB conversion; pix.save() as .png
  then raises "unsupported colorspace", silently dropped by the surrounding
  except. Fixed to `pix.n - pix.alpha >= 4` (correctly converts CMYK, leaves
  RGBA untouched).

- pipeline.py: detect_strategy([]) (an empty/whitespace-only source file)
  returned "content_based", routing into the PDF-oriented TOC-detection
  pipeline -- wasting a real LLM call before raising IndexingError. Empty
  node lists now route to level_based, whose build_tree_from_levels([])
  returns an empty structure instantly with zero LLM calls.

- page_index.py (shim): pageindex/__init__.py binds the canonical `page_index`
  function as the package attribute, but this file is ALSO a real submodule
  of the same name -- importing it anywhere (import machinery, unconditional)
  overwrites that attribute with the module object, breaking
  `from pageindex import page_index; page_index(x)` for the rest of the
  process. Made the shim module itself callable (delegates to the real
  function via a ModuleType subclass), so whichever object ends up in that
  slot is callable regardless of import order.

- storage/sqlite.py: create_collection let a raw sqlite3.IntegrityError escape
  on a duplicate name (new CollectionAlreadyExistsError); the collections
  table's CHECK constraint only validated the name's first character (GLOB
  '*' is a wildcard, not a regex quantifier over the preceding class) --
  fixed to validate the whole string, and SQLiteStorage now also validates in
  Python (it's a public StorageEngine usable directly, bypassing
  LocalBackend's own check).

- tests/test_review_fixes_2.py: two tests used a ContentNode with no `level`
  set, so build_index took the content_based path and made real (retried,
  slow, and -- with a valid key -- billable) LLM calls instead of testing the
  text-stripping logic they claimed to. Mocked out _content_based_pipeline.

- retrieve.py: _parse_pages/_get_pdf_page_content were independent copies of
  the canonical parse_pages/get_pdf_page_content that had already drifted
  (missing the p>=1 filter and 1000-page DoS cap) -- delegate to canonical
  now, so the legacy pageindex.get_page_content path can't silently regress
  again.

- parser/markdown.py: a leading UTF-8 BOM broke first-header detection
  (not whitespace, .strip() doesn't remove it) -- decode utf-8-sig. Only
  backtick fences were recognized as code blocks, so a '#'-prefixed line
  inside a ~~~-fenced block (valid CommonMark) was misparsed as a heading --
  recognize both fence styles.

- run_pageindex.py: --if-thinning wasn't migrated to the bare-flag +
  legacy-yes/no convention the other four --if-add-* flags got; bare usage
  raised an argparse error and it never went through the shared coercion.

- types.py: DocumentDetail's `structure` field was inside the class's
  total=False body, so TypedDict rules made it optional even though every
  backend always populates it. Split into a required base class.

Adds regression tests for all of the above. Full suite: 244 passed, 2 skipped
(one pre-existing, unrelated flaky cloud-streaming test).

Claude-Session: https://claude.ai/code/session_01Kx5DgKbhK1N8autqXH8SmS

tests/test_markdown_parser.py

@@ -71,3 +71,32 @@ def test_headerless_file_yields_single_node(tmp_path):
     assert len(result.nodes) == 1
     assert result.nodes[0].title == "plain"
     assert "No headings at all" in result.nodes[0].content
+
+
+def test_utf8_bom_does_not_break_the_first_header(tmp_path):
+    """A leading BOM (common from Windows editors/exporters) isn't
+    whitespace, so .strip() doesn't remove it — without utf-8-sig decoding,
+    the header regex fails to match the BOM-prefixed first line, and it gets
+    misclassified as unrecognized preamble text instead of a real heading."""
+    md = tmp_path / "bom.md"
+    md.write_bytes(b"\xef\xbb\xbf# First Header\nbody text\n")
+    result = MarkdownParser().parse(str(md))
+    assert len(result.nodes) == 1
+    assert result.nodes[0].title == "First Header"
+    assert result.nodes[0].level == 1
+
+
+def test_tilde_fenced_code_blocks_are_recognized(tmp_path):
+    """CommonMark allows both backtick and tilde code fences. Only
+    recognizing backticks let a '#'-prefixed line inside a ~~~-fenced block
+    (e.g. a shell comment in a sample) be misparsed as a real heading."""
+    md = tmp_path / "tilde.md"
+    md.write_text(
+        "# Real Header\nintro\n"
+        "~~~\n# not a real header, just a comment\n~~~\n"
+        "## Real Sub\nmore\n"
+    )
+    result = MarkdownParser().parse(str(md))
+    titles = [n.title for n in result.nodes]
+    assert titles == ["Real Header", "Real Sub"]
+    assert "not a real header" not in " ".join(n.title for n in result.nodes)