feat(extraction): R language support (#828) (#839)

R has no declaration syntax — everything is an expression — so the
extractor works through the visitNode hook: functions in every
assignment form (incl. nested, attributed to their enclosing scope),
top-level variables/constants, library()/require() imports and
source() file references (claimed, Lua-style), S4/RefClass/R6/ggproto
classes with their methods and extends edges, setGeneric/setMethod.
Grammar vendored from r-lib/tree-sitter-r v1.2.0 (ABI 14; npm package
is a security placeholder, tree-sitter-wasms has no R).

Benchmarked on AnomalyDetection (8/8 named defs), dplyr (1027 fns),
ggplot2 (150 ggproto classes / 597 methods / 128 extends edges —
adding ggproto mid-bench flipped the large-repo A/B from a regression
to 2.4x faster than the no-codegraph arm).

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

.claude/skills/agent-eval/corpus.json

@@ -1,98 +1,427 @@
 {
   "_comment": "Test corpus for /agent-eval. Add entries freely. size: Small (<~150 files), Medium (~150-1500), Large (>~1500). 'question' is a representative architectural question that exercises cross-file understanding.",
   "TypeScript": [
-    { "name": "ky", "repo": "https://github.com/sindresorhus/ky", "size": "Small", "files": "~25", "question": "How does ky implement request retries and timeouts?" },
-    { "name": "excalidraw", "repo": "https://github.com/excalidraw/excalidraw", "size": "Medium", "files": "~600", "question": "How does Excalidraw render and update canvas elements?" },
-    { "name": "vscode", "repo": "https://github.com/microsoft/vscode", "size": "Large", "files": "~10000", "question": "How does the extension host communicate with the main process?" }
+    {
+      "name": "ky",
+      "repo": "https://github.com/sindresorhus/ky",
+      "size": "Small",
+      "files": "~25",
+      "question": "How does ky implement request retries and timeouts?"
+    },
+    {
+      "name": "excalidraw",
+      "repo": "https://github.com/excalidraw/excalidraw",
+      "size": "Medium",
+      "files": "~600",
+      "question": "How does Excalidraw render and update canvas elements?"
+    },
+    {
+      "name": "vscode",
+      "repo": "https://github.com/microsoft/vscode",
+      "size": "Large",
+      "files": "~10000",
+      "question": "How does the extension host communicate with the main process?"
+    }
   ],
   "JavaScript": [
-    { "name": "express", "repo": "https://github.com/expressjs/express", "size": "Small", "files": "~50", "question": "How does Express route a request through its middleware stack?" }
+    {
+      "name": "express",
+      "repo": "https://github.com/expressjs/express",
+      "size": "Small",
+      "files": "~50",
+      "question": "How does Express route a request through its middleware stack?"
+    }
   ],
   "Go": [
-    { "name": "cobra", "repo": "https://github.com/spf13/cobra", "size": "Small", "files": "~50", "question": "How does cobra parse commands and flags?" },
-    { "name": "gin", "repo": "https://github.com/gin-gonic/gin", "size": "Medium", "files": "~150", "question": "How does gin route requests through its middleware chain?" },
-    { "name": "terraform", "repo": "https://github.com/hashicorp/terraform", "size": "Large", "files": "~4000", "question": "How does Terraform build and walk the resource dependency graph?" },
-    { "name": "cosmos-sdk", "repo": "https://github.com/cosmos/cosmos-sdk", "size": "Large", "files": "~5000", "question": "How does a bank module MsgSend message reach the account balance update? Trace the cross-module call path from the bank keeper's Send handler through to the account/balance store update." }
+    {
+      "name": "cobra",
+      "repo": "https://github.com/spf13/cobra",
+      "size": "Small",
+      "files": "~50",
+      "question": "How does cobra parse commands and flags?"
+    },
+    {
+      "name": "gin",
+      "repo": "https://github.com/gin-gonic/gin",
+      "size": "Medium",
+      "files": "~150",
+      "question": "How does gin route requests through its middleware chain?"
+    },
+    {
+      "name": "terraform",
+      "repo": "https://github.com/hashicorp/terraform",
+      "size": "Large",
+      "files": "~4000",
+      "question": "How does Terraform build and walk the resource dependency graph?"
+    },
+    {
+      "name": "cosmos-sdk",
+      "repo": "https://github.com/cosmos/cosmos-sdk",
+      "size": "Large",
+      "files": "~5000",
+      "question": "How does a bank module MsgSend message reach the account balance update? Trace the cross-module call path from the bank keeper's Send handler through to the account/balance store update."
+    }
   ],
   "Python": [
-    { "name": "click", "repo": "https://github.com/pallets/click", "size": "Small", "files": "~60", "question": "How does click parse command-line arguments into commands?" },
-    { "name": "flask", "repo": "https://github.com/pallets/flask", "size": "Medium", "files": "~90", "question": "How does Flask dispatch a request to a view function?" },
-    { "name": "django", "repo": "https://github.com/django/django", "size": "Large", "files": "~2700", "question": "How does Django's ORM build and execute a query from a QuerySet?" }
+    {
+      "name": "click",
+      "repo": "https://github.com/pallets/click",
+      "size": "Small",
+      "files": "~60",
+      "question": "How does click parse command-line arguments into commands?"
+    },
+    {
+      "name": "flask",
+      "repo": "https://github.com/pallets/flask",
+      "size": "Medium",
+      "files": "~90",
+      "question": "How does Flask dispatch a request to a view function?"
+    },
+    {
+      "name": "django",
+      "repo": "https://github.com/django/django",
+      "size": "Large",
+      "files": "~2700",
+      "question": "How does Django's ORM build and execute a query from a QuerySet?"
+    }
   ],
   "Rust": [
-    { "name": "clap", "repo": "https://github.com/clap-rs/clap", "size": "Medium", "files": "~200", "question": "How does clap parse arguments against a derived command definition?" },
-    { "name": "tokio", "repo": "https://github.com/tokio-rs/tokio", "size": "Large", "files": "~700", "question": "How does tokio schedule and run async tasks on its runtime?" },
-    { "name": "deno", "repo": "https://github.com/denoland/deno", "size": "Large", "files": "~1500", "question": "How does Deno load and execute a TypeScript module?" }
+    {
+      "name": "clap",
+      "repo": "https://github.com/clap-rs/clap",
+      "size": "Medium",
+      "files": "~200",
+      "question": "How does clap parse arguments against a derived command definition?"
+    },
+    {
+      "name": "tokio",
+      "repo": "https://github.com/tokio-rs/tokio",
+      "size": "Large",
+      "files": "~700",
+      "question": "How does tokio schedule and run async tasks on its runtime?"
+    },
+    {
+      "name": "deno",
+      "repo": "https://github.com/denoland/deno",
+      "size": "Large",
+      "files": "~1500",
+      "question": "How does Deno load and execute a TypeScript module?"
+    }
   ],
   "Java": [
-    { "name": "gson", "repo": "https://github.com/google/gson", "size": "Medium", "files": "~200", "question": "How does Gson serialize an object to JSON?" },
-    { "name": "okhttp", "repo": "https://github.com/square/okhttp", "size": "Medium", "files": "~640", "question": "How does OkHttp process a request through its interceptor chain?" },
-    { "name": "guava", "repo": "https://github.com/google/guava", "size": "Large", "files": "~3000", "question": "How does Guava's CacheBuilder build and configure a cache?" }
+    {
+      "name": "gson",
+      "repo": "https://github.com/google/gson",
+      "size": "Medium",
+      "files": "~200",
+      "question": "How does Gson serialize an object to JSON?"
+    },
+    {
+      "name": "okhttp",
+      "repo": "https://github.com/square/okhttp",
+      "size": "Medium",
+      "files": "~640",
+      "question": "How does OkHttp process a request through its interceptor chain?"
+    },
+    {
+      "name": "guava",
+      "repo": "https://github.com/google/guava",
+      "size": "Large",
+      "files": "~3000",
+      "question": "How does Guava's CacheBuilder build and configure a cache?"
+    }
   ],
   "Kotlin": [
-    { "name": "koin", "repo": "https://github.com/InsertKoinIO/koin", "size": "Medium", "files": "~300", "question": "How does Koin resolve and inject dependencies?" },
-    { "name": "leakcanary", "repo": "https://github.com/square/leakcanary", "size": "Medium", "files": "~250", "question": "How does LeakCanary detect and analyze a memory leak?" }
+    {
+      "name": "koin",
+      "repo": "https://github.com/InsertKoinIO/koin",
+      "size": "Medium",
+      "files": "~300",
+      "question": "How does Koin resolve and inject dependencies?"
+    },
+    {
+      "name": "leakcanary",
+      "repo": "https://github.com/square/leakcanary",
+      "size": "Medium",
+      "files": "~250",
+      "question": "How does LeakCanary detect and analyze a memory leak?"
+    }
   ],
   "Swift": [
-    { "name": "alamofire", "repo": "https://github.com/Alamofire/Alamofire", "size": "Small", "files": "~100", "question": "How does Alamofire build, send, and validate a request?" }
+    {
+      "name": "alamofire",
+      "repo": "https://github.com/Alamofire/Alamofire",
+      "size": "Small",
+      "files": "~100",
+      "question": "How does Alamofire build, send, and validate a request?"
+    }
   ],
   "C#": [
-    { "name": "serilog", "repo": "https://github.com/serilog/serilog", "size": "Medium", "files": "~250", "question": "How does Serilog route a log event to its sinks?" },
-    { "name": "jellyfin", "repo": "https://github.com/jellyfin/jellyfin", "size": "Large", "files": "~2500", "question": "How does Jellyfin scan and identify items in a media library?" }
+    {
+      "name": "serilog",
+      "repo": "https://github.com/serilog/serilog",
+      "size": "Medium",
+      "files": "~250",
+      "question": "How does Serilog route a log event to its sinks?"
+    },
+    {
+      "name": "jellyfin",
+      "repo": "https://github.com/jellyfin/jellyfin",
+      "size": "Large",
+      "files": "~2500",
+      "question": "How does Jellyfin scan and identify items in a media library?"
+    }
   ],
   "Ruby": [
-    { "name": "sinatra", "repo": "https://github.com/sinatra/sinatra", "size": "Small", "files": "~60", "question": "How does Sinatra match a request to a route handler?" },
-    { "name": "discourse", "repo": "https://github.com/discourse/discourse", "size": "Large", "files": "~3000", "question": "How does Discourse create and render a new post?" }
+    {
+      "name": "sinatra",
+      "repo": "https://github.com/sinatra/sinatra",
+      "size": "Small",
+      "files": "~60",
+      "question": "How does Sinatra match a request to a route handler?"
+    },
+    {
+      "name": "discourse",
+      "repo": "https://github.com/discourse/discourse",
+      "size": "Large",
+      "files": "~3000",
+      "question": "How does Discourse create and render a new post?"
+    }
   ],
   "PHP": [
-    { "name": "slim", "repo": "https://github.com/slimphp/Slim", "size": "Small", "files": "~80", "question": "How does Slim handle a request through its middleware?" },
-    { "name": "laravel", "repo": "https://github.com/laravel/framework", "size": "Large", "files": "~3000", "question": "How does Laravel resolve and dispatch a route to a controller?" }
+    {
+      "name": "slim",
+      "repo": "https://github.com/slimphp/Slim",
+      "size": "Small",
+      "files": "~80",
+      "question": "How does Slim handle a request through its middleware?"
+    },
+    {
+      "name": "laravel",
+      "repo": "https://github.com/laravel/framework",
+      "size": "Large",
+      "files": "~3000",
+      "question": "How does Laravel resolve and dispatch a route to a controller?"
+    }
   ],
   "C": [
-    { "name": "redis", "repo": "https://github.com/redis/redis", "size": "Large", "files": "~600", "question": "How does Redis parse and dispatch a client command?" }
+    {
+      "name": "redis",
+      "repo": "https://github.com/redis/redis",
+      "size": "Large",
+      "files": "~600",
+      "question": "How does Redis parse and dispatch a client command?"
+    }
   ],
   "C++": [
-    { "name": "json", "repo": "https://github.com/nlohmann/json", "size": "Small", "files": "~100", "question": "How does nlohmann::json parse a JSON string into a value?" },
-    { "name": "grpc", "repo": "https://github.com/grpc/grpc", "size": "Large", "files": "~3000", "question": "How does gRPC dispatch an incoming RPC to its handler?" }
+    {
+      "name": "json",
+      "repo": "https://github.com/nlohmann/json",
+      "size": "Small",
+      "files": "~100",
+      "question": "How does nlohmann::json parse a JSON string into a value?"
+    },
+    {
+      "name": "grpc",
+      "repo": "https://github.com/grpc/grpc",
+      "size": "Large",
+      "files": "~3000",
+      "question": "How does gRPC dispatch an incoming RPC to its handler?"
+    }
   ],
   "Dart": [
-    { "name": "flutter", "repo": "https://github.com/flutter/flutter", "size": "Large", "files": "~6000", "question": "How does Flutter build and lay out a widget tree?" }
+    {
+      "name": "flutter",
+      "repo": "https://github.com/flutter/flutter",
+      "size": "Large",
+      "files": "~6000",
+      "question": "How does Flutter build and lay out a widget tree?"
+    }
   ],
   "Svelte": [
-    { "name": "shadcn-svelte", "repo": "https://github.com/huntabyte/shadcn-svelte", "size": "Medium", "files": "~600", "question": "How do shadcn-svelte components compose and apply their styling?" }
+    {
+      "name": "shadcn-svelte",
+      "repo": "https://github.com/huntabyte/shadcn-svelte",
+      "size": "Medium",
+      "files": "~600",
+      "question": "How do shadcn-svelte components compose and apply their styling?"
+    }
   ],
   "Lua": [
-    { "name": "lualine.nvim", "repo": "https://github.com/nvim-lualine/lualine.nvim", "size": "Small", "files": "~120", "question": "How does lualine assemble and render its statusline sections and components?" },
-    { "name": "telescope.nvim", "repo": "https://github.com/nvim-telescope/telescope.nvim", "size": "Medium", "files": "~80", "question": "How does Telescope wire a picker to its finder, sorter, and previewer?" },
-    { "name": "kong", "repo": "https://github.com/Kong/kong", "size": "Large", "files": "~1330", "question": "How does Kong execute plugins across a request's lifecycle phases?" }
+    {
+      "name": "lualine.nvim",
+      "repo": "https://github.com/nvim-lualine/lualine.nvim",
+      "size": "Small",
+      "files": "~120",
+      "question": "How does lualine assemble and render its statusline sections and components?"
+    },
+    {
+      "name": "telescope.nvim",
+      "repo": "https://github.com/nvim-telescope/telescope.nvim",
+      "size": "Medium",
+      "files": "~80",
+      "question": "How does Telescope wire a picker to its finder, sorter, and previewer?"
+    },
+    {
+      "name": "kong",
+      "repo": "https://github.com/Kong/kong",
+      "size": "Large",
+      "files": "~1330",
+      "question": "How does Kong execute plugins across a request's lifecycle phases?"
+    }
   ],
   "Luau": [
-    { "name": "Knit", "repo": "https://github.com/Sleitnick/Knit", "size": "Small", "files": "~10", "question": "How does Knit register services and expose them to clients?" },
-    { "name": "vide", "repo": "https://github.com/centau/vide", "size": "Small", "files": "~40", "question": "How does vide track reactive sources and re-run effects when state changes?" },
-    { "name": "Fusion", "repo": "https://github.com/dphfox/Fusion", "size": "Medium", "files": "~115", "question": "How does Fusion build and update its reactive UI graph from state objects?" }
+    {
+      "name": "Knit",
+      "repo": "https://github.com/Sleitnick/Knit",
+      "size": "Small",
+      "files": "~10",
+      "question": "How does Knit register services and expose them to clients?"
+    },
+    {
+      "name": "vide",
+      "repo": "https://github.com/centau/vide",
+      "size": "Small",
+      "files": "~40",
+      "question": "How does vide track reactive sources and re-run effects when state changes?"
+    },
+    {
+      "name": "Fusion",
+      "repo": "https://github.com/dphfox/Fusion",
+      "size": "Medium",
+      "files": "~115",
+      "question": "How does Fusion build and update its reactive UI graph from state objects?"
+    }
   ],
   "Objective-C": [
-    { "name": "Masonry", "repo": "https://github.com/SnapKit/Masonry", "size": "Small", "files": "~50", "question": "How does Masonry build and activate Auto Layout constraints from its block DSL?" },
-    { "name": "FMDB", "repo": "https://github.com/ccgus/fmdb", "size": "Medium", "files": "~80", "question": "How does FMDB execute a prepared SQL statement and bind parameters?" },
-    { "name": "SDWebImage", "repo": "https://github.com/SDWebImage/SDWebImage", "size": "Large", "files": "~400", "question": "How does SDWebImage download, cache, and decode an image for a UIImageView?" }
+    {
+      "name": "Masonry",
+      "repo": "https://github.com/SnapKit/Masonry",
+      "size": "Small",
+      "files": "~50",
+      "question": "How does Masonry build and activate Auto Layout constraints from its block DSL?"
+    },
+    {
+      "name": "FMDB",
+      "repo": "https://github.com/ccgus/fmdb",
+      "size": "Medium",
+      "files": "~80",
+      "question": "How does FMDB execute a prepared SQL statement and bind parameters?"
+    },
+    {
+      "name": "SDWebImage",
+      "repo": "https://github.com/SDWebImage/SDWebImage",
+      "size": "Large",
+      "files": "~400",
+      "question": "How does SDWebImage download, cache, and decode an image for a UIImageView?"
+    }
   ],
   "Mixed iOS (Swift+ObjC)": [
-    { "name": "Charts", "repo": "https://github.com/danielgindi/Charts", "size": "Small", "files": "~270", "question": "How does the ChartsDemo ObjC demo controller drive the Swift Charts library to animate and notify a data update?" },
-    { "name": "realm-swift", "repo": "https://github.com/realm/realm-swift", "size": "Medium", "files": "~370", "question": "How does a Swift `Realm.write { realm.add(obj) }` reach the Objective-C persistence layer?" },
-    { "name": "wikipedia-ios", "repo": "https://github.com/wikimedia/wikipedia-ios", "size": "Large", "files": "~1700", "question": "How does tapping a search result reach the article-fetch network call across the Swift / ObjC boundary?" }
+    {
+      "name": "Charts",
+      "repo": "https://github.com/danielgindi/Charts",
+      "size": "Small",
+      "files": "~270",
+      "question": "How does the ChartsDemo ObjC demo controller drive the Swift Charts library to animate and notify a data update?"
+    },
+    {
+      "name": "realm-swift",
+      "repo": "https://github.com/realm/realm-swift",
+      "size": "Medium",
+      "files": "~370",
+      "question": "How does a Swift `Realm.write { realm.add(obj) }` reach the Objective-C persistence layer?"
+    },
+    {
+      "name": "wikipedia-ios",
+      "repo": "https://github.com/wikimedia/wikipedia-ios",
+      "size": "Large",
+      "files": "~1700",
+      "question": "How does tapping a search result reach the article-fetch network call across the Swift / ObjC boundary?"
+    }
   ],
   "React Native (legacy bridge + TurboModule)": [
-    { "name": "@react-native-async-storage", "repo": "https://github.com/react-native-async-storage/async-storage", "size": "Small", "files": "~60", "question": "How does `setItem` in JS reach the native `legacy_multiSet` implementation?" },
-    { "name": "react-native-svg", "repo": "https://github.com/software-mansion/react-native-svg", "size": "Medium", "files": "~700", "question": "How does a JS `Svg.getTotalLength(...)` reach the iOS / Android native implementation via TurboModule?" },
-    { "name": "react-native-firebase", "repo": "https://github.com/invertase/react-native-firebase", "size": "Large", "files": "~1100", "question": "How does a native iOS push notification reach the JS `messaging().onMessage(...)` listener?" }
+    {
+      "name": "@react-native-async-storage",
+      "repo": "https://github.com/react-native-async-storage/async-storage",
+      "size": "Small",
+      "files": "~60",
+      "question": "How does `setItem` in JS reach the native `legacy_multiSet` implementation?"
+    },
+    {
+      "name": "react-native-svg",
+      "repo": "https://github.com/software-mansion/react-native-svg",
+      "size": "Medium",
+      "files": "~700",
+      "question": "How does a JS `Svg.getTotalLength(...)` reach the iOS / Android native implementation via TurboModule?"
+    },
+    {
+      "name": "react-native-firebase",
+      "repo": "https://github.com/invertase/react-native-firebase",
+      "size": "Large",
+      "files": "~1100",
+      "question": "How does a native iOS push notification reach the JS `messaging().onMessage(...)` listener?"
+    }
   ],
   "Expo Modules": [
-    { "name": "expo-haptics", "repo": "https://github.com/expo/expo/tree/main/packages/expo-haptics", "size": "Small", "files": "~15", "question": "How does `Haptics.notificationAsync(...)` in JS reach `UINotificationFeedbackGenerator` in the Swift Module?" },
-    { "name": "expo-camera", "repo": "https://github.com/expo/expo/tree/main/packages/expo-camera", "size": "Medium", "files": "~70", "question": "How does a JS `CameraView.takePictureAsync(options)` reach the native AVCaptureSession / CameraDevice call?" }
+    {
+      "name": "expo-haptics",
+      "repo": "https://github.com/expo/expo/tree/main/packages/expo-haptics",
+      "size": "Small",
+      "files": "~15",
+      "question": "How does `Haptics.notificationAsync(...)` in JS reach `UINotificationFeedbackGenerator` in the Swift Module?"
+    },
+    {
+      "name": "expo-camera",
+      "repo": "https://github.com/expo/expo/tree/main/packages/expo-camera",
+      "size": "Medium",
+      "files": "~70",
+      "question": "How does a JS `CameraView.takePictureAsync(options)` reach the native AVCaptureSession / CameraDevice call?"
+    }
   ],
   "React Native Fabric (view components)": [
-    { "name": "react-native-segmented-control", "repo": "https://github.com/react-native-segmented-control/segmented-control", "size": "Small", "files": "~25", "question": "How does JSX `<SegmentedControl onChange={cb}/>` reach the native onChange handler on iOS/Android?" },
-    { "name": "react-native-screens", "repo": "https://github.com/software-mansion/react-native-screens", "size": "Medium", "files": "~1200", "question": "How does JSX `<ScreenStack>` reach the native RNSScreenStackView component?" },
-    { "name": "react-native-skia", "repo": "https://github.com/Shopify/react-native-skia", "size": "Large", "files": "~1000", "question": "How does a `<SkiaPictureView/>` JSX usage reach the iOS / Android native renderer?" }
+    {
+      "name": "react-native-segmented-control",
+      "repo": "https://github.com/react-native-segmented-control/segmented-control",
+      "size": "Small",
+      "files": "~25",
+      "question": "How does JSX `<SegmentedControl onChange={cb}/>` reach the native onChange handler on iOS/Android?"
+    },
+    {
+      "name": "react-native-screens",
+      "repo": "https://github.com/software-mansion/react-native-screens",
+      "size": "Medium",
+      "files": "~1200",
+      "question": "How does JSX `<ScreenStack>` reach the native RNSScreenStackView component?"
+    },
+    {
+      "name": "react-native-skia",
+      "repo": "https://github.com/Shopify/react-native-skia",
+      "size": "Large",
+      "files": "~1000",
+      "question": "How does a `<SkiaPictureView/>` JSX usage reach the iOS / Android native renderer?"
+    }
+  ],
+  "R": [
+    {
+      "name": "AnomalyDetection",
+      "repo": "https://github.com/twitter/AnomalyDetection",
+      "size": "Small",
+      "files": "~24",
+      "question": "How does AnomalyDetectionTs go from the exported entry function to the underlying S-H-ESD statistical test? Name the functions on the path in order."
+    },
+    {
+      "name": "dplyr",
+      "repo": "https://github.com/tidyverse/dplyr",
+      "size": "Medium",
+      "files": "~450",
+      "question": "When mutate() is called on a grouped data frame, which functions handle the grouping and expression evaluation, in order, from mutate() down?"
+    },
+    {
+      "name": "ggplot2",
+      "repo": "https://github.com/tidyverse/ggplot2",
+      "size": "Large",
+      "files": "~1150",
+      "question": "When a ggplot object is printed, how does the plot actually get built and drawn \u2014 trace the path from print/plot to where geoms render. Name the key functions in order."
+    }
   ]
-}
+}