Auto-generated API doc: doxygen → custom Python emitter → doc/api/.

`cmake --build build --target doc` runs Doxygen to produce XML, then
`doc/gen_api_md.py` (~330 lines, stdlib-only) emits a Markdown tree
under `doc/api/` that gitea renders directly in its file browser.

- 24 class/struct pages + 51 source-file pages + indices, with source
  links of the form `../../../../src/...#L42` that gitea turns into
  clickable line-anchored links.
- Doxyfile.in templated by CMake (XML-only output to build/doc/xml/).
- Pure Python emitter, zero external deps — no doxybook2 (not packaged
  on Arch) and no moxygen (avoids Node).
- Target gracefully disabled if Doxygen or Python 3 is missing at
  configure time; regular build target unaffected.

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

doc/Doxyfile.in

@@ -0,0 +1,55 @@
+# Doxygen configuration for essim — produces XML only, consumed by
+# doxybook2 to generate the Markdown tree under doc/api/.
+# Substituted by CMake (`configure_file ... @ONLY`).
+
+PROJECT_NAME           = "@PROJECT_NAME@"
+PROJECT_NUMBER         = "@PROJECT_VERSION@"
+PROJECT_BRIEF          = "@PROJECT_DESCRIPTION@"
+
+OUTPUT_DIRECTORY       = @DOXYGEN_OUTPUT_DIR@
+INPUT                  = @CMAKE_SOURCE_DIR@/src
+RECURSIVE              = YES
+FILE_PATTERNS          = *.hpp *.cpp *.h
+EXCLUDE_PATTERNS       = */build/* */build/_deps/*
+
+# We only need XML; doxybook2 will turn that into Markdown.
+GENERATE_HTML          = NO
+GENERATE_LATEX         = NO
+GENERATE_XML           = YES
+XML_OUTPUT             = xml
+XML_PROGRAMLISTING     = NO
+
+# Extraction policy — include everything the user can usefully reach, but
+# keep private implementation details out by default.
+EXTRACT_ALL            = YES
+EXTRACT_PRIVATE        = NO
+EXTRACT_STATIC         = YES
+EXTRACT_LOCAL_CLASSES  = YES
+EXTRACT_ANON_NSPACES   = NO
+
+# Comment style — the existing code uses Doxygen-flavoured `///` and
+# `/** … */`, both of which Doxygen recognises by default. JAVADOC_AUTOBRIEF
+# lets a single-line comment serve as the brief description.
+JAVADOC_AUTOBRIEF      = YES
+QT_AUTOBRIEF           = YES
+MULTILINE_CPP_IS_BRIEF = YES
+
+# Preprocess macros (forward declarations, #pragma once, etc.).
+ENABLE_PREPROCESSING   = YES
+MACRO_EXPANSION        = NO
+
+# Warnings — be helpful but not noisy.
+QUIET                  = YES
+WARN_IF_UNDOCUMENTED   = NO
+WARN_IF_DOC_ERROR      = YES
+WARN_NO_PARAMDOC       = NO
+
+# Diagrams — Graphviz isn't needed for Markdown output; doxybook2 ignores
+# image references unless explicitly handled. Keep DOT off so the build
+# stays light.
+HAVE_DOT               = NO
+
+# Mainpage — link the top-level README so doxybook2 picks it up as the
+# landing page in doc/api/.
+USE_MDFILE_AS_MAINPAGE = @CMAKE_SOURCE_DIR@/README.md
+INPUT                 += @CMAKE_SOURCE_DIR@/README.md @CMAKE_SOURCE_DIR@/DESIGN.md