test(r): pin the non-indexed R file types and the experimental classification

- Replace the vacuous ".Rprofile/.Renviron are not indexed" test (no fixture
  contained such files) with an r-non-indexed fixture holding .Rprofile,
  .Renviron, .Rmd and .qmd that define functions next to a plain .R positive
  control; the Rmd/qmd bodies are valid R so routing them to the R parser would
  fail the test.
- Add getLanguageFromFilename negatives for those names.
- Add R to the query-compilation smoke list.
- Assert R's LanguageClassifications value ('experimental'), which the docs
  claim but nothing checked.

gitnexus/test/fixtures/lang-resolution/r-non-indexed/.Renviron

@@ -0,0 +1 @@
+R_LIBS_USER=~/R/library

gitnexus/test/fixtures/lang-resolution/r-non-indexed/.Rprofile

@@ -0,0 +1 @@
+rprofile_fn <- function() 1

gitnexus/test/fixtures/lang-resolution/r-non-indexed/analysis.Rmd

@@ -0,0 +1,3 @@
+# Valid R on purpose: if this extension were ever routed to the R parser the
+# function below would be indexed, so the negative test can actually fail.
+rmd_fn <- function() 1

gitnexus/test/fixtures/lang-resolution/r-non-indexed/real.R

@@ -0,0 +1,2 @@
+# Positive control: a plain .R file is indexed.
+indexed_control <- function() 1

gitnexus/test/fixtures/lang-resolution/r-non-indexed/report.qmd

@@ -0,0 +1,2 @@
+# Valid R on purpose (see analysis.Rmd).
+qmd_fn <- function() 1

gitnexus/test/integration/query-compilation.test.ts

@@ -34,6 +34,7 @@ describe('Query compilation smoke tests', () => {
     [SupportedLanguages.Kotlin]: 'Test.kt',
     [SupportedLanguages.Swift]: 'test.swift',
     [SupportedLanguages.Dart]: 'test.dart',
+    [SupportedLanguages.R]: 'test.R',
   };
 
   // Known query compilation failures — remove from this set as PRs fix them

gitnexus/test/integration/resolvers/r.test.ts

@@ -374,20 +374,44 @@ describe('R function definitions and calls', () => {
     expect(itemsField).toBeDefined();
     expect(itemsField!.properties.visibility).toBe('public');
   });
+});
 
-  // --- Negative tests ---
+/**
+ * Files the R provider must not index. The `r-non-indexed` fixture holds a
+ * `.Rprofile`, `.Renviron`, `.Rmd` and `.qmd`, each defining a function, next to a plain
+ * `real.R` positive control (docs/languages/r-provider.md, "Limits").
+ */
+describe('R files that are not indexed', () => {
+  let result: PipelineResult;
 
-  it('does not index .Rprofile or .Renviron files', () => {
-    const allNodes: string[] = [];
-    result.graph.forEachNode((n) => {
-      if (
-        n.properties.filePath?.includes('.Rprofile') ||
-        n.properties.filePath?.includes('.Renviron')
-      ) {
-        allNodes.push(n.properties.name);
-      }
-    });
-    expect(allNodes).toHaveLength(0);
+  beforeAll(async () => {
+    result = await runPipelineFromRepo(path.join(FIXTURES, 'r-non-indexed'), () => {});
+  }, 60000);
+
+  it('indexes the plain .R control file (so the negatives below are not vacuous)', () => {
+    expect(getNodesByLabel(result, 'Function')).toEqual(['indexed_control']);
+  });
+
+  // The scanner may still record a bare File node for these; what must not exist is any
+  // parsed symbol (Function, Variable, ...) from them.
+  it.each(['.Rprofile', '.Renviron', 'analysis.Rmd', 'report.qmd'])(
+    'creates no symbol node for %s',
+    (name) => {
+      const hits: string[] = [];
+      result.graph.forEachNode((n) => {
+        if (n.label !== 'File' && n.properties.filePath?.endsWith(name)) {
+          hits.push(`${n.label}:${n.properties.name}`);
+        }
+      });
+      expect(hits).toEqual([]);
+    },
+  );
+
+  it('defines no function from the non-indexed files', () => {
+    const functions = getNodesByLabel(result, 'Function');
+    expect(functions).not.toContain('rprofile_fn');
+    expect(functions).not.toContain('rmd_fn');
+    expect(functions).not.toContain('qmd_fn');
   });
 });
 

gitnexus/test/unit/ingestion-utils.test.ts

@@ -159,6 +159,18 @@ describe('getLanguageFromFilename', () => {
     it.each(['.r', '.R'])('detects %s files', (ext) => {
       expect(getLanguageFromFilename(`analysis${ext}`)).toBe(SupportedLanguages.R);
     });
+
+    // docs/languages/r-provider.md: only `.r` / `.R` are handled.
+    it.each([
+      'analysis.Rmd',
+      'report.qmd',
+      '.Rprofile',
+      '.Renviron',
+      'Rprofile.site',
+      'x.Rhistory',
+    ])('returns null for %s', (name) => {
+      expect(getLanguageFromFilename(name)).toBeNull();
+    });
   });
 
   describe('unsupported', () => {

gitnexus/test/unit/r-language-classification.test.ts

@@ -0,0 +1,16 @@
+import { describe, expect, it } from 'vitest';
+import { LanguageClassifications, isProductionLanguage } from 'gitnexus-shared';
+import { SupportedLanguages } from '../../src/config/supported-languages.js';
+
+// docs/languages/r-provider.md describes R as an experimental provider. The classification
+// map is type-forced to contain R but nothing else asserts its value, so a silent
+// promotion to 'production' (a governance change) would otherwise go unnoticed.
+describe('R language classification', () => {
+  it('classifies R as experimental', () => {
+    expect(LanguageClassifications[SupportedLanguages.R]).toBe('experimental');
+  });
+
+  it('does not treat R as a production language', () => {
+    expect(isProductionLanguage(SupportedLanguages.R)).toBe(false);
+  });
+});