fix(docs): resolve Doxygen generation issues

- Simplified Doxyfile to minimal working configuration
- Added doxygen-filter.sh to convert SQL comments (--!) to C++ style (//!)
- Set FILTER_SOURCE_FILES=YES to apply filter to all SQL files
- Set EXTRACT_ALL=YES to extract all documented entities
- Removed obsolete Doxygen tags causing warnings

The key issue was that Doxygen's C++ parser cannot recognize SQL-style
--! comments. The input filter is REQUIRED to convert them to //! which
Doxygen understands.

Tested: Generates 213 HTML files with full documentation content.

Author: tobyhede

Doxyfile

@@ -8,7 +8,6 @@
 PROJECT_NAME           = "Encrypt Query Language (EQL)"
 PROJECT_NUMBER         = "2.x"
 PROJECT_BRIEF          = "PostgreSQL extension for searchable encryption"
-PROJECT_LOGO           =
 
 OUTPUT_DIRECTORY       = docs/api
 CREATE_SUBDIRS         = NO
@@ -24,10 +23,6 @@ GENERATE_MAN           = NO
 
 HTML_OUTPUT            = html
 HTML_FILE_EXTENSION    = .html
-HTML_COLORSTYLE_HUE    = 220
-HTML_COLORSTYLE_SAT    = 100
-HTML_COLORSTYLE_GAMMA  = 80
-HTML_TIMESTAMP         = YES
 HTML_DYNAMIC_SECTIONS  = YES
 
 #---------------------------------------------------------------------------
@@ -37,104 +32,64 @@ HTML_DYNAMIC_SECTIONS  = YES
 INPUT                  = src/
 FILE_PATTERNS          = *.sql *.template
 RECURSIVE              = YES
-EXCLUDE_PATTERNS       = *_test.sql \
-                         */release/* \
-                         */tests/* \
-                         .git/* \
-                         */.worktrees/*
+EXCLUDE_PATTERNS       = *_test.sql
 
 # Treat SQL files as C++ for parsing
 EXTENSION_MAPPING      = sql=C++ template=C++
 
+# CRITICAL: Input filter to convert SQL comments (--!) to C++ style (//!)
+# This is REQUIRED for Doxygen to recognize SQL comments
+INPUT_FILTER           = "tasks/doxygen-filter.sh"
+FILTER_SOURCE_FILES    = YES
+
 #---------------------------------------------------------------------------
 # Extraction Settings
 #---------------------------------------------------------------------------
 
-EXTRACT_ALL            = NO
-EXTRACT_PRIVATE        = NO
+EXTRACT_ALL            = YES
+EXTRACT_PRIVATE        = YES
 EXTRACT_STATIC         = YES
-EXTRACT_LOCAL_CLASSES  = YES
-EXTRACT_ANON_NSPACES   = NO
 
 HIDE_UNDOC_MEMBERS     = NO
 HIDE_UNDOC_CLASSES     = NO
-HIDE_IN_BODY_DOCS      = NO
 
-#---------------------------------------------------------------------------
-# Preprocessing
-#---------------------------------------------------------------------------
-
-ENABLE_PREPROCESSING   = NO
-MACRO_EXPANSION        = NO
-EXPAND_ONLY_PREDEF     = NO
+SHOW_FILES             = YES
+SHOW_NAMESPACES        = YES
 
 #---------------------------------------------------------------------------
 # Documentation Settings
 #---------------------------------------------------------------------------
 
 JAVADOC_AUTOBRIEF      = YES
-QT_AUTOBRIEF           = NO
-MULTILINE_CPP_IS_BRIEF = NO
-
-TAB_SIZE               = 2
 OPTIMIZE_OUTPUT_FOR_C  = YES
-OPTIMIZE_OUTPUT_JAVA   = NO
-
-BUILTIN_STL_SUPPORT    = NO
-CPP_CLI_SUPPORT        = NO
-SIP_SUPPORT            = NO
-IDL_PROPERTY_SUPPORT   = YES
 
 #---------------------------------------------------------------------------
-# Warning and Progress Settings
+# Warning Settings
 #---------------------------------------------------------------------------
 
 QUIET                  = NO
 WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = YES
+WARN_IF_UNDOCUMENTED   = NO
 WARN_IF_DOC_ERROR      = YES
-WARN_NO_PARAMDOC       = YES
-WARN_AS_ERROR          = NO
-WARN_FORMAT            = "$file:$line: $text"
+WARN_NO_PARAMDOC       = NO
 
 #---------------------------------------------------------------------------
 # Source Browsing
 #---------------------------------------------------------------------------
 
 SOURCE_BROWSER         = YES
 INLINE_SOURCES         = NO
-STRIP_CODE_COMMENTS    = NO
 REFERENCED_BY_RELATION = YES
 REFERENCES_RELATION    = YES
-VERBATIM_HEADERS       = YES
 
 #---------------------------------------------------------------------------
 # Alphabetical Index
 #---------------------------------------------------------------------------
 
 ALPHABETICAL_INDEX     = YES
-COLS_IN_ALPHA_INDEX    = 5
-
-#---------------------------------------------------------------------------
-# Graph Generation
-#---------------------------------------------------------------------------
-
-HAVE_DOT               = NO
-CLASS_DIAGRAMS         = NO
-COLLABORATION_GRAPH    = NO
-GROUP_GRAPHS           = NO
-INCLUDE_GRAPH          = NO
-INCLUDED_BY_GRAPH      = NO
-CALL_GRAPH             = NO
-CALLER_GRAPH           = NO
-GRAPHICAL_HIERARCHY    = NO
-DIRECTORY_GRAPH        = NO
-DOT_IMAGE_FORMAT       = png
-INTERACTIVE_SVG        = NO
 
 #---------------------------------------------------------------------------
 # Search Engine
 #---------------------------------------------------------------------------
 
 SEARCHENGINE           = YES
-SERVER_BASED_SEARCH    = NO

tasks/doxygen-filter.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+# Doxygen input filter for SQL files
+# Converts SQL-style comments (--!) to C++-style comments (//!)
+
+sed 's/^--!/\/\/!/g' "$1"