feat(r): add conservative semantic rename provider

Plain R functions rename through the scope graph; S3, string-spelled,
S4, R6 and NAMESPACE-exported names are refused. Adds fixtures, the
rename-provider-r test and its cross-platform shard entries.

docs/languages/r-provider.md

@@ -111,6 +111,20 @@ Not modelled:
 - `stop()`, `on.exit()`, `tryCatch` handlers and other non-local exits are ordinary calls: no throw edges and no finaliser routing. A `break` / `next` with no enclosing loop falls back to EXIT.
 - Function join: a CFG is anchored at the `function_definition` token, while the `Function` node starts at the whole assignment. They share a start line for `f <- function`, `f = function` and `f <- \(x)`, but not for `f <-` followed by `function` on the next line; there the CFG is still emitted and its blocks lie inside the `Function` node's span, but the exact start-line join used by taint summaries does not resolve (inert for R today, since reaching definitions have no facts). Anonymous functions have a CFG but no `Function` node.
 
+## Rename
+
+`languages/r/rename.ts` gives the `rename` tool a deliberately narrow, fail-closed R provider (fixtures under `test/fixtures/rename-integration/r/`). R binds names dynamically, so only what the scope graph proves is renamed.
+
+- **Succeeds:** a plain function (`name <- function(...)`) and the calls the graph resolves to it, in one file or across files. A same-named parameter is claimed as a binding and left alone.
+- **Refused (`unsupported_occurrence`, planning status `unsupported`):**
+  - any target that is not a plain `Function` (S4 classes, R6 classes, members);
+  - a function whose old or new name is spelled as a string literal anywhere in the indexed R sources (`UseMethod("area")`, `do.call("f", ...)`, `match.fun`, `get`, `setGeneric`, ...), because string lookup is not resolved;
+  - a new name `generic.class` whose prefix is an existing function, which would register an S3 method;
+  - a package function under `R/` that `NAMESPACE` does not mark private (`isExported` is not false), because `NAMESPACE` is not an indexed source and its `export()` or `S3method()` entry would go stale.
+- **Refused by the shared engine (fail-closed, not provider code):** S3 methods and any dotted function name (`area.circle` reads as an owner-qualified member, so `stale_graph`); S4 class names (`unsupported_occurrence`, no exact source-name span); R6 methods (`stale_graph`).
+- **Invalid names (`invalid_name`):** anything that is not a nonreserved R identifier.
+- **Not proven:** unqualified calls to a function defined in another file (including the package `R/` layout) fail with `ambiguous_reference`, because R's global-name fallback is not a provable binding. Renaming across files works only where the call is qualified or otherwise resolved.
+
 ## Type annotations
 
 R has no inline type annotations, so the "Type Annotations" column of the language support table is not ticked for R. The roxygen2 `@param` extraction above is a comment-based fallback, in the same class as the JSDoc, PHPDoc and YARD fallbacks listed in type-resolution-system.md (Ruby's YARD support is likewise not ticked).

gitnexus/scripts/cross-platform-shard.ts

@@ -62,6 +62,7 @@ export const WINDOWS_WEIGHTS_SEC: Readonly<Record<string, number>> = {
   'test/integration/rename-provider-objective-c.test.ts': 285,
   'test/integration/rename-provider-php.test.ts': 100,
   'test/integration/rename-provider-python.test.ts': 375,
+  'test/integration/rename-provider-r.test.ts': 100,
   'test/integration/rename-provider-ruby.test.ts': 100,
   'test/integration/rename-provider-rust.test.ts': 75,
   'test/integration/rename-provider-swift.test.ts': 300,

gitnexus/scripts/cross-platform-tests.ts

@@ -170,6 +170,7 @@ const LBUG_NATIVE = [
   'test/integration/rename-provider-objective-c.test.ts',
   'test/integration/rename-provider-php.test.ts',
   'test/integration/rename-provider-python.test.ts',
+  'test/integration/rename-provider-r.test.ts',
   'test/integration/rename-provider-ruby.test.ts',
   'test/integration/rename-provider-rust.test.ts',
   'test/integration/rename-provider-swift.test.ts',

gitnexus/src/core/ingestion/languages/r.ts

@@ -20,6 +20,7 @@ import { rPostParse } from './r/post-parse.js';
 import { rDefinitionProperties, rResolveMemberOwnerNode } from './r/owner-hooks.js';
 import { isRNonNamingArgumentCapture } from './r/naming-argument.js';
 import { createRCfgVisitor } from '../cfg/visitors/r.js';
+import { rRenameProvider } from './r/rename.js';
 
 const R_BUILT_INS: ReadonlySet<string> = new Set([
   // Base R
@@ -195,4 +196,5 @@ export const rProvider = defineLanguage({
   shouldSkipDefinitionCapture: isRNonNamingArgumentCapture,
   // Control flow only (no def/use harvest): CFG + CDG, REACHING_DEF reports no-facts.
   cfgVisitor: createRCfgVisitor(),
+  rename: rRenameProvider,
 });

gitnexus/src/core/ingestion/languages/r/rename.ts

@@ -0,0 +1,106 @@
+import type { NameClaim } from 'gitnexus-shared';
+import type { RenameIssue, RenameProvider } from '../../rename-provider.js';
+import {
+  createTreeSitterRenameSource,
+  innermostRenameScope,
+  walkNamedNodes,
+} from '../rename-tree-sitter.js';
+
+/**
+ * Conservative semantic rename for R. Plain functions are renamed through the
+ * scope-resolution graph. R binds names dynamically (S3/S4/R6 dispatch, strings,
+ * NAMESPACE), so every declaration or name that the graph cannot prove is refused.
+ */
+const RESERVED = new Set(
+  'if else repeat while function for next break TRUE FALSE NULL Inf NaN NA NA_integer_ NA_real_ NA_character_ NA_complex_ in'.split(
+    ' ',
+  ),
+);
+
+const unsupported = (message: string): RenameIssue => ({
+  code: 'unsupported_occurrence',
+  status: 'unsupported',
+  message,
+});
+
+const parseNames = createTreeSitterRenameSource({
+  isName: (node) => node.type === 'identifier',
+  skip: (node) => node.type === 'comment',
+  role: (node) =>
+    node.parent?.type === 'parameter' && node.parent.childForFieldName('name')?.id === node.id
+      ? 'binding'
+      : 'name',
+});
+
+export const rRenameProvider: RenameProvider = {
+  validateName(name) {
+    if (!/^(?:[A-Za-z]|\.(?![0-9]))[A-Za-z0-9._]*$/.test(name) || RESERVED.has(name))
+      return { code: 'invalid_name', message: 'Choose a valid nonreserved R identifier.' };
+  },
+  async parseSource(input) {
+    const source = await parseNames(input);
+    // Parameters shadow same-named functions: claim them per scope so the engine
+    // leaves an unrelated parameter alone.
+    const claims = new Map<string, NameClaim[]>();
+    for (const occurrence of source.occurrences) {
+      if (occurrence.role !== 'binding' || !occurrence.node) continue;
+      const scope = innermostRenameScope(source.parsed, occurrence.node);
+      if (!scope) continue;
+      claims.set(scope, [
+        ...(claims.get(scope) ?? []),
+        {
+          name: occurrence.name,
+          range: occurrence.range,
+          kind: 'binding',
+          hoisted: true,
+          purpose: 'value',
+        },
+      ]);
+    }
+    return {
+      ...source,
+      parsed: {
+        ...source.parsed,
+        scopes: source.parsed.scopes.map((scope) => ({
+          ...scope,
+          nameClaims: [...(scope.nameClaims ?? []), ...(claims.get(scope.id) ?? [])],
+        })),
+      },
+    };
+  },
+  checkSafety({ target, newName, files, graph }) {
+    const name = target.qualifiedName ?? '';
+    if (target.type !== 'Function')
+      return unsupported('Only plain R functions can be renamed; classes and members are refused.');
+    const defined = new Set(
+      [...files.values()].flatMap((source) => source.parsed.localDefs.map((d) => d.qualifiedName)),
+    );
+    if (newName.includes('.') && defined.has(newName.slice(0, newName.indexOf('.'))))
+      return unsupported('The new name would register an S3 method of an existing function.');
+    for (const source of files.values()) {
+      if (!source.tree) continue;
+      for (const node of walkNamedNodes(source.tree.rootNode)) {
+        if (node.type === 'string_content' && (node.text === name || node.text === newName))
+          return unsupported(
+            'A string literal spells this name; S3, S4, R6 and dynamic lookup resolve it by string.',
+          );
+      }
+    }
+    // NAMESPACE is not an indexed source. A package function that the NAMESPACE
+    // exports (the graph keeps isExported unless it is proven private) is refused.
+    const file = target.filePath;
+    let exported = false;
+    graph.forEachNode((node) => {
+      if (
+        node.properties.filePath === file &&
+        node.properties.name === name &&
+        node.properties.isExported !== false
+      )
+        exported = true;
+    });
+    if (exported && /(^|\/)R\//.test(file))
+      return unsupported(
+        'A package function may have a NAMESPACE export entry that is not renamed.',
+      );
+  },
+};

gitnexus/test/fixtures/rename-integration/r/function-call-chain/after/chain.R

@@ -0,0 +1,10 @@
+assist <- function(v) v + 1
+
+step <- function(v) {
+  assist(assist(v))
+}
+
+# helper is described here
+main <- function() {
+  step(1)
+}

gitnexus/test/fixtures/rename-integration/r/function-call-chain/before/chain.R

@@ -0,0 +1,10 @@
+helper <- function(v) v + 1
+
+step <- function(v) {
+  helper(helper(v))
+}
+
+# helper is described here
+main <- function() {
+  step(1)
+}

gitnexus/test/fixtures/rename-integration/r/function-call-chain/case.json

@@ -0,0 +1,15 @@
+{
+  "language": "r",
+  "description": "Rename a plain function called twice in one expression; a comment mentioning the name is untouched.",
+  "categories": ["call-graph", "same-file", "comments"],
+  "target": { "name": "helper", "kind": "Function", "file": "chain.R", "startLine": 0 },
+  "newName": "assist",
+  "expect": { "status": "success", "edits": 3 },
+  "edges": [
+    {
+      "type": "CALLS",
+      "from": { "name": "step", "kind": "Function", "file": "chain.R", "startLine": 2 },
+      "to": { "name": "helper", "kind": "Function", "file": "chain.R", "startLine": 0 }
+    }
+  ]
+}

gitnexus/test/fixtures/rename-integration/r/function-unrelated-parameter/after/apply.R

@@ -0,0 +1,3 @@
+apply_twice <- function(compute, v) {
+  compute(compute(v))
+}

gitnexus/test/fixtures/rename-integration/r/function-unrelated-parameter/after/lib.R

@@ -0,0 +1,7 @@
+calculate <- function(x) {
+  x * 2
+}
+
+run <- function(y) {
+  calculate(y) + 1
+}

gitnexus/test/fixtures/rename-integration/r/function-unrelated-parameter/before/apply.R

@@ -0,0 +1,3 @@
+apply_twice <- function(compute, v) {
+  compute(compute(v))
+}

gitnexus/test/fixtures/rename-integration/r/function-unrelated-parameter/before/lib.R

@@ -0,0 +1,7 @@
+compute <- function(x) {
+  x * 2
+}
+
+run <- function(y) {
+  compute(y) + 1
+}

gitnexus/test/fixtures/rename-integration/r/function-unrelated-parameter/case.json

@@ -0,0 +1,15 @@
+{
+  "language": "r",
+  "description": "Rename a plain function called in its own file while a same-named parameter in a second file is left alone.",
+  "categories": ["call-graph", "cross-file", "parameter-shadowing"],
+  "target": { "name": "compute", "kind": "Function", "file": "lib.R", "startLine": 0 },
+  "newName": "calculate",
+  "expect": { "status": "success", "edits": 2 },
+  "edges": [
+    {
+      "type": "CALLS",
+      "from": { "name": "run", "kind": "Function", "file": "lib.R", "startLine": 4 },
+      "to": { "name": "compute", "kind": "Function", "file": "lib.R", "startLine": 0 }
+    }
+  ]
+}

gitnexus/test/fixtures/rename-integration/r/invalid-name-invalid-start/after/lib.R

@@ -0,0 +1,3 @@
+tick <- function(x) x + 1
+
+run <- function() tick(1)

gitnexus/test/fixtures/rename-integration/r/invalid-name-invalid-start/before/lib.R

@@ -0,0 +1,3 @@
+tick <- function(x) x + 1
+
+run <- function() tick(1)

gitnexus/test/fixtures/rename-integration/r/invalid-name-invalid-start/case.json

@@ -0,0 +1,9 @@
+{
+  "language": "r",
+  "description": "Refuse a name starting with a digit as the new function name.",
+  "categories": ["identifier-rules", "negative", "unchanged-on-error"],
+  "target": { "name": "tick", "kind": "Function", "file": "lib.R", "startLine": 0 },
+  "newName": "2fast",
+  "expect": { "status": "error", "code": "invalid_name", "planningStatus": "blocked" },
+  "edges": []
+}

gitnexus/test/fixtures/rename-integration/r/invalid-name-reserved-word/after/lib.R

@@ -0,0 +1,3 @@
+tick <- function(x) x + 1
+
+run <- function() tick(1)

gitnexus/test/fixtures/rename-integration/r/invalid-name-reserved-word/before/lib.R

@@ -0,0 +1,3 @@
+tick <- function(x) x + 1
+
+run <- function() tick(1)

gitnexus/test/fixtures/rename-integration/r/invalid-name-reserved-word/case.json

@@ -0,0 +1,9 @@
+{
+  "language": "r",
+  "description": "Refuse a reserved word as the new function name.",
+  "categories": ["identifier-rules", "negative", "unchanged-on-error"],
+  "target": { "name": "tick", "kind": "Function", "file": "lib.R", "startLine": 0 },
+  "newName": "repeat",
+  "expect": { "status": "error", "code": "invalid_name", "planningStatus": "blocked" },
+  "edges": []
+}

gitnexus/test/fixtures/rename-integration/r/namespace-export/after/DESCRIPTION

@@ -0,0 +1,3 @@
+Package: pk
+Version: 0.1.0
+Title: Fixture

gitnexus/test/fixtures/rename-integration/r/namespace-export/after/NAMESPACE

@@ -0,0 +1 @@
+export(compute)

gitnexus/test/fixtures/rename-integration/r/namespace-export/after/R/lib.R

@@ -0,0 +1,5 @@
+compute <- function(x) {
+  x * 2
+}
+
+use_it <- function() compute(2)

gitnexus/test/fixtures/rename-integration/r/namespace-export/before/DESCRIPTION

@@ -0,0 +1,3 @@
+Package: pk
+Version: 0.1.0
+Title: Fixture

gitnexus/test/fixtures/rename-integration/r/namespace-export/before/NAMESPACE

@@ -0,0 +1 @@
+export(compute)

gitnexus/test/fixtures/rename-integration/r/namespace-export/before/R/lib.R

@@ -0,0 +1,5 @@
+compute <- function(x) {
+  x * 2
+}
+
+use_it <- function() compute(2)

gitnexus/test/fixtures/rename-integration/r/namespace-export/case.json

@@ -0,0 +1,9 @@
+{
+  "language": "r",
+  "description": "Refuse a package function that NAMESPACE exports, because the export entry would go stale.",
+  "categories": ["namespace", "package-export", "negative", "unchanged-on-error"],
+  "target": { "name": "compute", "kind": "Function", "file": "R/lib.R", "startLine": 0 },
+  "newName": "calculate",
+  "expect": { "status": "error", "code": "unsupported_occurrence", "planningStatus": "unsupported" },
+  "edges": []
+}

gitnexus/test/fixtures/rename-integration/r/r6-class/after/account.R

@@ -0,0 +1,11 @@
+Account <- R6::R6Class("Account",
+  public = list(
+    balance = 0,
+    deposit = function(n) {
+      self$balance <- self$balance + n
+      invisible(self)
+    }
+  )
+)
+
+acc <- Account$new()

gitnexus/test/fixtures/rename-integration/r/r6-class/before/account.R

@@ -0,0 +1,11 @@
+Account <- R6::R6Class("Account",
+  public = list(
+    balance = 0,
+    deposit = function(n) {
+      self$balance <- self$balance + n
+      invisible(self)
+    }
+  )
+)
+
+acc <- Account$new()

gitnexus/test/fixtures/rename-integration/r/r6-class/case.json

@@ -0,0 +1,9 @@
+{
+  "language": "r",
+  "description": "Refuse an R6 class whose members and constructor are reached through $new and self.",
+  "categories": ["r6", "class", "negative", "unchanged-on-error"],
+  "target": { "name": "Account", "kind": "Class", "file": "account.R", "startLine": 0 },
+  "newName": "Wallet",
+  "expect": { "status": "error", "code": "unsupported_occurrence", "planningStatus": "unsupported" },
+  "edges": []
+}

gitnexus/test/fixtures/rename-integration/r/s3-generic/after/shapes.R

@@ -0,0 +1,5 @@
+area <- function(x) UseMethod("area")
+
+area.circle <- function(x) 3.14 * x$r^2
+
+total <- function(s) area(s)

gitnexus/test/fixtures/rename-integration/r/s3-generic/before/shapes.R

@@ -0,0 +1,5 @@
+area <- function(x) UseMethod("area")
+
+area.circle <- function(x) 3.14 * x$r^2
+
+total <- function(s) area(s)

gitnexus/test/fixtures/rename-integration/r/s3-generic/case.json

@@ -0,0 +1,9 @@
+{
+  "language": "r",
+  "description": "Refuse an S3 generic whose UseMethod string and area.circle method dispatch by spelling.",
+  "categories": ["s3", "string-dispatch", "negative", "unchanged-on-error"],
+  "target": { "name": "area", "kind": "Function", "file": "shapes.R", "startLine": 0 },
+  "newName": "surface",
+  "expect": { "status": "error", "code": "unsupported_occurrence", "planningStatus": "unsupported" },
+  "edges": []
+}

gitnexus/test/fixtures/rename-integration/r/s3-method/after/shapes.R

@@ -0,0 +1,3 @@
+area <- function(x) UseMethod("area")
+
+area.circle <- function(x) 3.14 * x$r^2

gitnexus/test/fixtures/rename-integration/r/s3-method/before/shapes.R

@@ -0,0 +1,3 @@
+area <- function(x) UseMethod("area")
+
+area.circle <- function(x) 3.14 * x$r^2

gitnexus/test/fixtures/rename-integration/r/s3-method/case.json

@@ -0,0 +1,23 @@
+{
+  "language": "r",
+  "description": "Refuse an S3 method: its dotted name is read as an owner-qualified member, so the graph identity is not a unique source declaration.",
+  "categories": [
+    "s3",
+    "dotted-name",
+    "negative",
+    "unchanged-on-error"
+  ],
+  "target": {
+    "name": "area.circle",
+    "kind": "Function",
+    "file": "shapes.R",
+    "startLine": 2
+  },
+  "newName": "round_area",
+  "expect": {
+    "status": "error",
+    "code": "stale_graph",
+    "planningStatus": "blocked"
+  },
+  "edges": []
+}

gitnexus/test/fixtures/rename-integration/r/s3-new-method-name/after/shapes.R

@@ -0,0 +1,3 @@
+area <- function(x) 1
+
+circle_area <- function(x) 3.14 * x$r^2

gitnexus/test/fixtures/rename-integration/r/s3-new-method-name/before/shapes.R

@@ -0,0 +1,3 @@
+area <- function(x) 1
+
+circle_area <- function(x) 3.14 * x$r^2

gitnexus/test/fixtures/rename-integration/r/s3-new-method-name/case.json

@@ -0,0 +1,9 @@
+{
+  "language": "r",
+  "description": "Refuse a new dotted name whose prefix is an existing function, which would silently register an S3 method of it.",
+  "categories": ["s3", "name-collision", "negative", "unchanged-on-error"],
+  "target": { "name": "circle_area", "kind": "Function", "file": "shapes.R", "startLine": 2 },
+  "newName": "area.circle",
+  "expect": { "status": "error", "code": "unsupported_occurrence", "planningStatus": "unsupported" },
+  "edges": []
+}

gitnexus/test/fixtures/rename-integration/r/s4-class/after/person.R

@@ -0,0 +1,3 @@
+setClass("Person", representation(name = "character"))
+
+make <- function() new("Person", name = "a")

gitnexus/test/fixtures/rename-integration/r/s4-class/before/person.R

@@ -0,0 +1,3 @@
+setClass("Person", representation(name = "character"))
+
+make <- function() new("Person", name = "a")

gitnexus/test/fixtures/rename-integration/r/s4-class/case.json

@@ -0,0 +1,9 @@
+{
+  "language": "r",
+  "description": "Refuse an S4 class whose name is spelled only in string literals.",
+  "categories": ["s4", "class", "negative", "unchanged-on-error"],
+  "target": { "name": "Person", "kind": "Class", "file": "person.R", "startLine": 0 },
+  "newName": "Human",
+  "expect": { "status": "error", "code": "unsupported_occurrence", "planningStatus": "unsupported" },
+  "edges": []
+}

gitnexus/test/fixtures/rename-integration/r/string-lookup/after/dyn.R

@@ -0,0 +1,3 @@
+worker <- function(x) x + 1
+
+run <- function() do.call("worker", list(1))

gitnexus/test/fixtures/rename-integration/r/string-lookup/before/dyn.R

@@ -0,0 +1,3 @@
+worker <- function(x) x + 1
+
+run <- function() do.call("worker", list(1))

gitnexus/test/fixtures/rename-integration/r/string-lookup/case.json

@@ -0,0 +1,9 @@
+{
+  "language": "r",
+  "description": "Refuse a function that a string literal names for do.call dynamic lookup.",
+  "categories": ["string-dispatch", "negative", "unchanged-on-error"],
+  "target": { "name": "worker", "kind": "Function", "file": "dyn.R", "startLine": 0 },
+  "newName": "job",
+  "expect": { "status": "error", "code": "unsupported_occurrence", "planningStatus": "unsupported" },
+  "edges": []
+}

gitnexus/test/integration/rename-provider-r.test.ts

@@ -0,0 +1,3 @@
+import { defineRenameFixtureTests } from '../helpers/rename-integration-cases.js';
+
+defineRenameFixtureTests('r');