From a7ec43dbc61a5bb85ca8bdf9648c16396c4e5d67 Mon Sep 17 00:00:00 2001
From: Mick Cooney <mcooney@describedata.com>
Date: Thu, 1 Oct 2026 03:23:46 +0100
Subject: [PATCH] refactor(r): remove five dead patterns from R_QUERIES

The S4/R5 contains= (single and c()), R6 inherit= (namespaced and bare)
and (comment) patterns capture @heritage*, @comment, which no code
reads: such a match has no @name and no @definition.*, so the worker
discards it. Inheritance edges come from the R scope query's
@reference.inherits.

Graph nodes, relationships, properties, resolution outcomes and the raw
worker output are byte-identical over the r-* fixtures and probe repos
before and after, so no re-analyse and no SCHEMA_BUMP are needed.

Also correct the R scope query header, which described the legacy table
as having proved the heritage shapes.
---
 .../src/core/ingestion/languages/r/query.ts   |  7 ++-
 .../src/core/ingestion/tree-sitter-queries.ts | 61 -------------------
 2 files changed, 4 insertions(+), 64 deletions(-)

diff --git a/gitnexus/src/core/ingestion/languages/r/query.ts b/gitnexus/src/core/ingestion/languages/r/query.ts
index e5dbf20be..725988721 100644
--- a/gitnexus/src/core/ingestion/languages/r/query.ts
+++ b/gitnexus/src/core/ingestion/languages/r/query.ts
@@ -4,9 +4,10 @@
  * R has no dedicated class syntax — R6 classes are `R6Class(...)` calls, S4/R5
  * classes are `setClass(...)`/`setRefClass(...)` calls — so this query mirrors
  * the shapes the legacy `R_QUERIES` (`tree-sitter-queries.ts`) already proved
- * queryable for structural extraction, renamed onto the scope-resolution
- * capture vocabulary (`@scope.*`, `@declaration.*`, `@reference.*`,
- * `@import.*`, `@type-binding.*`).
+ * queryable for structural extraction (the heritage shapes below have no
+ * counterpart there), renamed onto the scope-resolution capture vocabulary
+ * (`@scope.*`, `@declaration.*`, `@reference.*`, `@import.*`,
+ * `@type-binding.*`).
  *
  * R specifics encoded here:
  *
diff --git a/gitnexus/src/core/ingestion/tree-sitter-queries.ts b/gitnexus/src/core/ingestion/tree-sitter-queries.ts
index 7ec15bf77..332cc73c5 100644
--- a/gitnexus/src/core/ingestion/tree-sitter-queries.ts
+++ b/gitnexus/src/core/ingestion/tree-sitter-queries.ts
@@ -3177,64 +3177,6 @@ export const R_QUERIES = `
     (argument
       value: [(identifier) (string)] @import.source))) @import
 
-; ── Heritage: S4 contains= (single parent) ───────────────────────────────────
-(call
-  function: (identifier) @_fn
-  (#match? @_fn "^(setClass|setRefClass)$")
-  arguments: (arguments
-    . (argument
-      value: (string
-        content: (string_content) @heritage.class))
-    (argument
-      name: (identifier) @_arg
-      (#match? @_arg "^(contains|CONTAINS)$")
-      value: (string
-        content: (string_content) @heritage.extends)))) @heritage
-
-; ── Heritage: S4 contains= (multiple parents via c()) ────────────────────────
-(call
-  function: (identifier) @_fn2
-  (#match? @_fn2 "^(setClass|setRefClass)$")
-  arguments: (arguments
-    . (argument
-      value: (string
-        content: (string_content) @heritage.class))
-    (argument
-      name: (identifier) @_arg2
-      (#match? @_arg2 "^(contains|CONTAINS)$")
-      value: (call
-        function: (identifier) @_cfn
-        (#match? @_cfn "^c$")
-        arguments: (arguments
-          (argument
-            value: (string
-              content: (string_content) @heritage.extends))))))) @heritage
-
-; ── Heritage: R6 inherit= via namespace ──────────────────────────────────────
-(binary_operator
-  lhs: (identifier) @heritage.class
-  rhs: (call
-    function: (namespace_operator
-      rhs: (identifier) @_nsfn
-      (#match? @_nsfn "^R6Class$"))
-    arguments: (arguments
-      (argument
-        name: (identifier) @_arg
-        (#match? @_arg "^inherit$")
-        value: (identifier) @heritage.extends)))) @heritage
-
-; ── Heritage: R6 inherit= via bare call ──────────────────────────────────────
-(binary_operator
-  lhs: (identifier) @heritage.class
-  rhs: (call
-    function: (identifier) @_r6fn
-    (#match? @_r6fn "^R6Class$")
-    arguments: (arguments
-      (argument
-        name: (identifier) @_arg
-        (#match? @_arg "^inherit$")
-        value: (identifier) @heritage.extends)))) @heritage
-
 ; ── R6 Fields via namespace (non-function entries in public/private list()) ──
 (binary_operator
   lhs: (identifier) @_class
@@ -3286,9 +3228,6 @@ export const R_QUERIES = `
         arguments: (arguments
           (argument
             name: (identifier) @name) @definition.property)))))
-
-; ── Roxygen2 doc comments ────────────────────────────────────────────────────
-(comment) @comment
 `;
 
 import { SupportedLanguages } from 'gitnexus-shared';