diff --git a/Doxyfile b/Doxyfile
index 3e5bb7209..0994f1097 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -45,7 +45,11 @@ XML_PROGRAMLISTING     = YES
 #---------------------------------------------------------------------------
 
 INPUT                  = src/
-FILE_PATTERNS          = *.sql *.template
+# Only the generated *.sql is documented. *.template files are build-time
+# sources (they still carry $RELEASE_VERSION placeholders and duplicate their
+# generated .sql), so documenting them produced a spurious second `version`
+# memberdef with placeholder text.
+FILE_PATTERNS          = *.sql
 RECURSIVE              = YES
 EXCLUDE_PATTERNS       = *_test.sql
 
diff --git a/src/v3/version.template b/src/v3/version.template
index 0849b0b08..828635352 100644
--- a/src/v3/version.template
+++ b/src/v3/version.template
@@ -21,10 +21,8 @@ DROP FUNCTION IF EXISTS eql_v3.version();
 --!
 --! @note Auto-generated during build from src/v3/version.template
 --!
---! @example
---! -- Check installed EQL version
---! SELECT eql_v3.version();
---! -- Returns: '3.0.0'
+--! Example: `SELECT eql_v3.version()` returns the installed version string,
+--! e.g. `'3.0.0'` (or `'DEV'` for development builds).
 CREATE FUNCTION eql_v3.version()
   RETURNS text
   IMMUTABLE STRICT PARALLEL SAFE
diff --git a/tasks/docs/doxygen-filter.sh b/tasks/docs/doxygen-filter.sh
index ab196dd9c..b64bd806a 100755
--- a/tasks/docs/doxygen-filter.sh
+++ b/tasks/docs/doxygen-filter.sh
@@ -1,5 +1,50 @@
 #!/usr/bin/env bash
 #MISE description="Doxygen input filter for SQL files"
+set -euo pipefail
 
-# Converts SQL-style comments (--!) to C++-style comments (//!)
-sed 's/^--!/\/\/!/g' "$1"
+# Doxygen always calls an INPUT_FILTER with exactly one filename. Guard it so a
+# stray invocation fails fast instead of `awk` blocking on stdin and hanging the
+# docs job.
+if [ "$#" -ne 1 ]; then
+  echo "usage: $(basename "$0") <file.sql>" >&2
+  exit 2
+fi
+
+# Prepares SQL for Doxygen's C++ parser. Two transforms:
+#
+#  1. `--!` doc comments -> `//!` so Doxygen sees them.
+#  2. Strip dollar-quoted function bodies (`$$ ... $$`), leaving just the
+#     declaration and its trailing clauses. Doxygen parses SQL heuristically as
+#     C++, and body SQL derails it: a `::type` cast reads as C++ scope
+#     resolution and drops the whole enclosing CREATE FUNCTION memberdef (this
+#     silently lost jsonb_path_query and ~hundreds of generated extractor
+#     overloads), while keywords/calls in bodies (`SELECT`, `RETURN NEXT`,
+#     `array_length(...)`) get mis-parsed as spurious functions. Bodies carry no
+#     documentation, so removing them is lossless for the generated reference
+#     and leaves Doxygen only clean `CREATE FUNCTION name(args) RETURNS ...`
+#     declarations to read. Only bare `$$` quoting is used in this codebase.
+awk '
+  /^--!/ { print "//!" substr($0, 4); next }
+  {
+    out = ""
+    s = $0
+    while (length(s) > 0) {
+      p = index(s, "$$")
+      if (inbody) {
+        if (p == 0) { s = ""; break }        # whole remainder is body: drop
+        s = substr(s, p + 2)                  # resume after the closing $$
+        inbody = 0
+      } else {
+        if (p == 0) { out = out s; break }    # no body marker: keep as-is
+        out = out substr(s, 1, p - 1)         # keep code before opening $$
+        s = substr(s, p + 2)
+        inbody = 1
+      }
+    }
+    # Regular SQL `--` comments read as C++ code to Doxygen (e.g.
+    # `-- per-entry overloads (...)` mints a phantom `overloads(...)` function),
+    # so neutralize them to C++ line comments on the (body-stripped) code.
+    gsub(/--/, "//", out)
+    print out
+  }
+' "$1"
diff --git a/tasks/docs/generate/test_xml_to_markdown.py b/tasks/docs/generate/test_xml_to_markdown.py
index 77fb6cd5a..c547c9703 100755
--- a/tasks/docs/generate/test_xml_to_markdown.py
+++ b/tasks/docs/generate/test_xml_to_markdown.py
@@ -155,6 +155,50 @@ def test_schema_qualified_type():
 
     print("✓ Schema-qualified type test passed")
 
+def _load_process_function():
+    """Load process_function from the hyphenated module by path."""
+    import importlib.util
+
+    spec = importlib.util.spec_from_file_location(
+        "eql_xml_to_markdown", Path(__file__).parent / "xml-to-markdown.py"
+    )
+    mod = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(mod)
+    return mod.process_function
+
+def test_internal_schema_is_private():
+    """Functions in the eql_v3_internal schema are flagged private via <type>.
+
+    Doxygen puts the schema in the memberdef <type> ("CREATE FUNCTION
+    eql_v3_internal"), not the <name>, so visibility is a schema check. Guards
+    against regressing to the old leading-underscore-name heuristic, which
+    flagged none of the internal surface (reporting everything public).
+    """
+    from xml.etree import ElementTree as ET
+
+    process_function = _load_process_function()
+
+    def memberdef(schema, fn):
+        return ET.fromstring(f'''
+        <memberdef kind="function">
+            <name>{fn}</name>
+            <type>CREATE FUNCTION {schema}</type>
+            <argsstring>(val jsonb) RETURNS bytea</argsstring>
+            <briefdescription><para>Extract a term.</para></briefdescription>
+            <detaileddescription></detaileddescription>
+        </memberdef>
+        ''')
+
+    internal = process_function(memberdef("eql_v3_internal", "eq_term"))
+    assert internal is not None, "internal function should be extracted"
+    assert internal["is_private"] is True, "eql_v3_internal.* must be private"
+
+    public = process_function(memberdef("eql_v3", "jsonb_path_query"))
+    assert public is not None, "public function should be extracted"
+    assert public["is_private"] is False, "eql_v3.* must be public"
+
+    print("✓ Internal-schema private detection test passed")
+
 if __name__ == '__main__':
     print("Running xml-to-markdown tests...\n")
 
@@ -163,6 +207,7 @@ def test_schema_qualified_type():
         test_variants_no_self_reference()
         test_param_name_type_swap()
         test_schema_qualified_type()
+        test_internal_schema_is_private()
 
         print("\n✅ All tests passed!")
         sys.exit(0)
diff --git a/tasks/docs/generate/xml-to-markdown.py b/tasks/docs/generate/xml-to-markdown.py
index 02ce371b5..f838547fc 100755
--- a/tasks/docs/generate/xml-to-markdown.py
+++ b/tasks/docs/generate/xml-to-markdown.py
@@ -203,8 +203,15 @@ def process_function(memberdef):
             if op_match:
                 func_name = op_match.group(1)  # Use operator as function name
 
-    # Check if this is a private/internal function
-    is_private = func_name.startswith('_')
+    # Check if this is a private/internal function.
+    # Internal functions live in the `eql_v3_internal` schema. Doxygen puts the
+    # schema in the memberdef <type> (e.g. "CREATE FUNCTION eql_v3_internal"),
+    # not the <name>, so a schema check is required — the older bare
+    # leading-underscore convention alone flags none of them (which left the
+    # whole surface reported as public). Keep the underscore check too.
+    type_elem = memberdef.find('type')
+    type_text = extract_para_text(type_elem) if type_elem is not None else ''
+    is_private = func_name.startswith('_') or 'eql_v3_internal' in type_text
 
     # Extract descriptions
     brief = extract_description(memberdef.find('briefdescription'))