docs(doxygen): fix critical extraction bug; baseline 24% → 42% on public API

ROOT CAUSE FIX
The Doxyfile EXCLUDE_PATTERNS line contained `*/* 2.hpp` (note the
space — a stray glob from macOS-style "foo 2.hpp" duplicate files).
That pattern was silently matching ALL .hpp / .h files, so Doxygen was
indexing nothing under code/include/.  The pre-existing 556 KB of HTML
output was effectively documenting only README.md, CLAUDE.md and a
small stub for std:: — not the C++ API at all.

After fixing the pattern (and properly escaping the space-prefixed
"foo 2.hpp / foo 2.h" macOS-dup patterns), Doxygen now extracts 141
compounds and emits 248 HTML pages from the public headers.

WHAT THIS PR ADDS
1. Doxyfile fix: correct EXCLUDE_PATTERNS; add GENERATE_XML for the
   coverage measurement script; add MathJax for `$$...$$` math in
   markdown; add the missing CGAL `\cgalParamNBegin/End/Description/
   Default/...` aliases so CGAL-style param blocks render correctly.

2. New headers:
   - code/include/CGAL/Conformal_map/doxygen_groups.h
     defines `PkgConformalMap{,Ref,Concepts,NamedParameters}`,
     resolving 17 prior "non-existing group" warnings.
   - code/include/CGAL/Conformal_map/doxygen_namespaces.h
     gives every namespace under `CGAL::` and `conformallab::` a
     brief description.

3. New tool: scripts/doxygen-coverage.sh
   Parses the XML output and reports % of public symbols (excluding
   the `detail::` implementation namespaces by default) that have a
   non-empty brief/detailed description.  Supports `--list-undoc`
   and `--threshold N` for CI integration.

4. Substantial docstring additions to the public CGAL headers:
   `Conformal_map_traits.h`, `Discrete_circle_packing.h`,
   `Discrete_inversive_distance.h`, `conformal_mesh.hpp`,
   `Discrete_conformal_map.h` (Hyper_ideal_map_result fields).

5. Markdown housekeeping that the strict-warning Doxygen run surfaced:
   tests.md (escape literal `#` in table cell),
   locked-vs-flexible.md (broken section anchor),
   overall_pipeline.md (replace `$$LaTeX$$` with inline-unicode math).

CURRENT NUMBERS

  before:  ~24%  documented (public API; the prior "87%" claim was
                 based on the broken extraction)
  after:    42%  documented   (165 of 396 public symbols)
  warnings: 0   (was 27 spurious + a flood of bogus undocumented
                  warnings hidden by the buggy EXCLUDE pattern)

NEXT (in a follow-up commit on this branch)
The remaining 231 public symbols (mostly in `layout.hpp`,
`hyper_ideal_functional.hpp`, `spherical_functional.hpp`, the per-mode
functional/Hessian files) can be brought to ~100% with another pass of
short `///` brief descriptions.  The coverage script is the gate; CI
can begin enforcing `--threshold 95` once the next pass lands.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Doxyfile

@@ -31,7 +31,15 @@ EXCLUDE_PATTERNS       = */build*/* \
                          */deps/* \
                          */.git/* \
                          */test-reports/* \
-                         */* 2.hpp
+                         *\ 2.hpp \
+                         *\ 2.h
+# Research-quality LaTeX notes use raw \sinh / \cosh / \frac / \beta /
+# \cdot / \partial / \zeta macros which are valid LaTeX but unknown to
+# Doxygen.  These files are intended to be read as PDF or in a LaTeX-
+# aware markdown viewer, not as Doxygen pages.  Excluding them removes
+# ~500 spurious "unknown command" warnings while keeping the .md files
+# discoverable on GitHub.
+EXCLUDE                = doc/math/hyperideal-hessian-derivation.md
 EXCLUDE_SYMBOLS        = Eigen::* boost::* std::*
 
 # Markdown filter: rewrites repo-relative links like [x](doc/api/tests.md)
@@ -70,7 +78,7 @@ EXTENSION_MAPPING      = h=C++ hpp=C++
 # ── Warnings ─────────────────────────────────────────────────────────────────
 QUIET                  = NO
 WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = NO
+WARN_IF_UNDOCUMENTED   = YES
 WARN_IF_DOC_ERROR      = YES
 WARN_IF_INCOMPLETE_DOC = YES
 WARN_NO_PARAMDOC       = NO
@@ -80,6 +88,16 @@ WARN_LOGFILE           = doc/doxygen/doxygen-warnings.log
 
 # ── HTML output ──────────────────────────────────────────────────────────────
 GENERATE_HTML          = YES
+
+# MathJax — render LaTeX math in markdown ($...$ and $$...$$) and in
+# code-comment `\f$ ... \f$` blocks via MathJax in the generated HTML.
+# Required for the conformal-mapping math notation (\Theta, \omega, \tau,
+# \mathbb{H}, …) in doc/architecture/overall_pipeline.md and the
+# header docstrings.
+USE_MATHJAX            = YES
+MATHJAX_VERSION        = MathJax_3
+MATHJAX_FORMAT         = HTML-CSS
+MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@3/es5/
 HTML_OUTPUT            = html
 HTML_FILE_EXTENSION    = .html
 HTML_COLORSTYLE        = LIGHT
@@ -100,7 +118,9 @@ SERVER_BASED_SEARCH    = NO
 GENERATE_LATEX         = NO
 GENERATE_RTF           = NO
 GENERATE_MAN           = NO
-GENERATE_XML           = NO
+GENERATE_XML           = YES
+XML_OUTPUT             = xml
+XML_PROGRAMLISTING     = NO
 GENERATE_DOCBOOK       = NO
 GENERATE_AUTOGEN_DEF   = NO
 GENERATE_PERLMOD       = NO
@@ -130,3 +150,16 @@ ALIASES               += "concept{1}=\xrefitem concept \"Concept\" \"Concepts\"
 ALIASES               += "models{1}=\xrefitem models \"Models\" \"Models\" \1"
 ALIASES               += "cgalRequires{1}=\par Requirements: \n\1"
 ALIASES               += "cgalParam{2}=\param \1 \2"
+# CGAL named-parameter block aliases — replicates the upstream
+# ${CGAL}/Documentation/doc/Documentation/Doxyfile_common conventions
+# so that \cgalParamNBegin{name} … \cgalParamNEnd blocks render as
+# nested HTML lists in our Doxygen output.
+ALIASES               += "cgalNamedParamsBegin=<dl class=\"params\"><dt>Optional named parameters</dt><dd><table class=\"params\">"
+ALIASES               += "cgalNamedParamsEnd=</table></dd></dl>"
+ALIASES               += "cgalParamNBegin{1}=<tr><td class=\"paramname\"><code>\1</code></td><td>"
+ALIASES               += "cgalParamNEnd=</td></tr>"
+ALIASES               += "cgalParamDescription{1}=<b>Description:</b> \1<br/>"
+ALIASES               += "cgalParamType{1}=<b>Type:</b> \1<br/>"
+ALIASES               += "cgalParamDefault{1}=<b>Default:</b> \1<br/>"
+ALIASES               += "cgalParamPrecondition{1}=<b>Precondition:</b> \1<br/>"
+ALIASES               += "cgalParamExtra{1}=<i>\1</i><br/>"