chore(deps): remove unused proprietary dep pymupdf-layout

pymupdf-layout is Artifex commercial-only proprietary (its wheel ships
only a one-line COPYING noting "Commercial license. See artifex.com"),
incompatible with the project's AGPL build. It was declared as a runtime
dependency but unused: not imported anywhere in nextcloud_mcp_server/ or
tests/.

Also drop tools/parse-doc.py, an unused dev scratch script that was the
only caller of pymupdf.layout.activate(). Per the explicit warning in
document_processors/pymupdf.py, activating layout breaks
pymupdf4llm.to_markdown(page_chunks=True) per pymupdf4llm#323.

Closes #725

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

pyproject.toml

@@ -41,7 +41,6 @@ dependencies = [
     "markdownify>=0.14.1",  # HTML to Markdown conversion for News items
     "pymupdf>=1.26.6",
     "pymupdf4llm>=0.2.2",
-    "pymupdf-layout>=1.26.6",
     "openai>=2.8.1",
     "dynaconf>=3.2.13,<4.0",
 ]