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

pageindex/parser/markdown.py

@@ -12,7 +12,12 @@ class MarkdownParser:
         path = Path(file_path)
         model = kwargs.get("model")
 
-        with open(path, "r", encoding="utf-8") as f:
+        # utf-8-sig strips a leading BOM if present (common from Windows
+        # editors/exporters) and is otherwise identical to plain utf-8. Without
+        # it, a BOM-prefixed first line fails the header regex below (the BOM
+        # isn't whitespace, so .strip() doesn't remove it), misclassifying the
+        # document's first heading as unrecognized preamble text.
+        with open(path, "r", encoding="utf-8-sig") as f:
             content = f.read()
 
         lines = content.split("\n")
@@ -23,7 +28,10 @@ class MarkdownParser:
 
     def _extract_headers(self, lines: list[str]) -> list[dict]:
         header_pattern = r"^(#{1,6})\s+(.+)$"
-        code_block_pattern = r"^```"
+        # CommonMark allows both backtick and tilde fences; only recognizing
+        # backticks let a '#'-prefixed line inside a ~~~-fenced block (e.g. a
+        # shell comment in a code sample) be misparsed as a real heading.
+        code_block_pattern = r"^(?:```|~~~)"
         headers = []
         in_code_block = False
 

pageindex/parser/pdf.py

@@ -77,7 +77,13 @@ class PdfParser:
 
                 try:
                     pix = pymupdf.Pixmap(image_bytes)
-                    if pix.n > 4:
+                    # n includes the alpha channel, so a plain RGBA pixmap also
+                    # has n==4 — subtract alpha before comparing. Without this,
+                    # a CMYK image with no alpha (n==4, same as RGBA) skips the
+                    # RGB conversion, and pix.save() as .png then raises
+                    # "unsupported colorspace for 'png'", silently dropping the
+                    # image via the bare except below.
+                    if pix.n - pix.alpha >= 4:
                         pix = pymupdf.Pixmap(pymupdf.csRGB, pix)
                     filename = f"p{page_num}_img{img_idx}.png"
                     save_path = images_path / filename