Add: R (.r/.R) language support via bespoke extract_r

[Sirhan1]

What

Adds R (.r/.R) language support via a new bespoke extract_r under graphify/extractors/, following the Julia (dd8235e) and Elixir (3d5da60) precedent. Scoped strictly to .R code structure + call topology — package metadata and package-qualified call resolution are deferred to a follow-up.

Why

R was the motivating case for the #1689 "no AST extractor" warning (.r/.R is in CODE_EXTENSIONS but had no dispatch entry). This PR wires a real extractor and reuses the existing #1745 install-extra warning path for the missing-dependency case (pip install "graphifyy[r]").

Named functions in R are assignments whose right- or left-hand side is an anonymous function_definition, so the generic extractor is not a good fit. A bespoke extractor under graphify/extractors/ matches the established home for language-specific extractors (not the extract.py god node).

No maintained tree-sitter-r wheel fits the repo's per-language wheel model, so the grammar ships via tree-sitter-language-pack>=1.12,<2 under the optional [r] extra. The pack may fetch/cache the R grammar on first use; no source is uploaded and R itself is not executed.

How

• Wiring: .r → _DISPATCH (.R reuses the existing case-insensitive suffix fallback); .r → _EXTRA_FOR_EXTENSION (names the [r] extra in #1745); .r → _LANG_FAMILY_BY_EXT as the "r" family (blocks cross-language binding); Rscript → _SHEBANG_DISPATCH (Rscript was already in _SHEBANG_CODE_INTERPRETERS, so R-shebang scripts were already detected as code — they now dispatch instead of hitting #1689). No new node types, relations, resolver interfaces, or package-ownership semantics; CODE_EXTENSIONS, _CASE_INSENSITIVE_EXTS, and the analysis family map unchanged.
• extract_r() emits the existing nodes/edges/raw_calls contract:
  • File node per parsed file; function nodes for all five assignment forms (<-, <<-, =, ->, ->>), scoped IDs for nested fns beneath the enclosing fn.
  • Rejects member assignments, computed targets, and = used as a named call argument.
  • Top-level calls attribute to the file; function-body calls attribute to the enclosing fn. Nested function bodies are skipped while walking an outer fn's calls (prevents double attribution).
  • $ / @ receiver calls and :: / ::: package-qualified calls become raw_calls with is_member_call=True, so the shared resolver won't bind them by method name.
  • Pipe expressions (|>, %>%) traverse normally so contained calls are captured.
  • Unqualified bare calls resolve same-file EXTRACTED; unresolved bare calls go to raw_calls for the shared cross-file resolver, which resolves a unique cross-file candidate EXTRACTED with import evidence or INFERRED without, leaving ambiguous names unresolved.
• Imports: library(pkg), require(pkg), requireNamespace("pkg") with a literal identifier or string → imports edges; pkg::fn / pkg:::fn double as import evidence for pkg. Dynamic expressions (call args, variables) are skipped.
• source("helper.r"): only a static string ending in .r (case-insensitive), resolved against the caller file's directory (mirrors the Bash static-source policy). Emits imports_from only when the target exists on disk. URLs, connections, variables, computed paths, and missing files are skipped.
• No R-specific resolver pass registered this phase; R unqualified calls reuse the shared cross-file resolver unchanged.

Tests

• tests/fixtures/sample.r + 3 cross-file fixtures (r_other.r, r_extra.r, r_caller.r).
• 22 R tests in tests/test_languages.py following the DM optional-grammar skip-when-unavailable convention (@_needs_r for real-grammar tests; dispatch/missing-dep tests stay network-free via monkeypatched sys.modules).
• 2 new tests in tests/test_extract.py (test_extract_warns_when_r_extra_missing, test_extract_no_warning_when_r_extra_installed).
• Two pre-existing test_extract.py tests that asserted .R/.r triggered #1689 now use .ejs (the canonical no-extractor case), since .R is now dispatched.

Real-grammar tests skip when tree-sitter-language-pack is absent. Tests must not download a parser implicitly; missing-dependency and dispatch tests are network-free.

Verification

• All R tests pass locally (22 + 13 test_extract tests, real grammar loaded).
• Full suite: 3250 passed, 3 skipped, 0 failures related to this change (one pre-existing flaky test_label_communities_batches_when_over_batch_size is order-dependent and fails on a clean stashed tree too — unrelated to R; there's already fix: make label batching test independent of order #1872 tracking it).
• ruff check clean on touched files.
• pyright clean on graphify/extractors/r.py (0 errors with the venv pythonpath; the import-resolution noise on tree_sitter_language_pack / tree_sitter is repo-wide pre-existing and affects every extractor identically).
• graphify update . run to refresh the graphify-out graph.

Scope deferred to follow-up (#9)

R package metadata (DESCRIPTION DCF ingestion, NAMESPACE imports/exports), package-qualified call resolution once package-to-symbol ownership exists, S3/S4/R6 semantics, .Rmd chunk extraction, NSE/formula handling, higher-order callback inference, renv.lock, and runtime evaluation.