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>

CHANGELOG.md

@@ -16,6 +16,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### New Features
 
+- **CodeGraph now indexes R** (`.R` / `.r`) — functions in every assignment form (`name <- function(...)`, `name = function(...)`, nested definitions), S4 / Reference / R6 classes with their methods, `setGeneric`/`setMethod` generics, top-level variables and constants, `library()` / `require()` imports, `source()` file references, and call edges — including calls inside tidyverse pipe chains. Statistical and research codebases get the full explore / impact / callers surface. (#828) (R)
 - **Workspaces holding multiple git repositories now index as a whole.** Running `codegraph init` at the root of a directory that contains several independent git repos — including the common "super-repo" layout where the parent repo's `.gitignore` hides the child repos to keep `git status` quiet — now indexes every nested project into one graph, with each child repo's own `.gitignore` respected. `codegraph sync` and live file watching pick up changes inside the nested repos too (previously change detection only consulted the parent repo, so edits in child repos were invisible until a full re-index). Git repositories inside `node_modules` (npm git-dependencies) remain excluded. (#514)
 
 - **`codegraph_explore` now explains where a flow ends instead of going silent.** When the symbols you ask about don't connect statically — because the code dispatches through a runtime mechanism like a computed call (`handlers[action.type](...)`), Python's `getattr`, a command/mediator bus (`sender.Send(new DeleteCommand(...))`), reflection, or `new Proxy` — explore now announces the exact dispatch site (file and line) where the static path stops, and when the dispatch key is visible in the source it shortlists the likely runtime targets (for example pointing a MediatR command straight at its `Handler.Handle` method). Detection is deterministic and runs only when a flow fails to connect; fully connected flows are unchanged, and nothing about indexing or the graph itself changes. Relatedly, a custom event bus whose emit and handler connect through a single synthesized hop now shows that hop explicitly (with the registration site) — it previously rendered nothing because the connection was "too short" for the flow section. (#687)