docs(r): correct the R capability note after NAMESPACE export support

README.md

@@ -704,11 +704,11 @@ GitNexus builds a complete knowledge graph of your codebase through a multi-phas
 | Objective-C | ✓      | —              | ✓       | ✓        | ✓                | —                     | —      | —          | —            |
 | Dart       | ✓       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
 | Zig        | ✓       | —              | ✓       | —        | ✓                | ✓                     | ✓      | —          | ✓            |
-| R (experimental) | ✓  | ✓              | —       | ✓        | ✓                | ✓                     | ✓      | —          | —            |
+| R (experimental) | ✓  | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | —          | —            |
 
 **Imports** — cross-file import resolution · **Named Bindings** — `import { X as Y }` / re-export tracking · **Exports** — public/exported symbol detection · **Heritage** — class inheritance, interfaces, mixins · **Type Annotations** — explicit type extraction for receiver resolution · **Constructor Inference** — infer receiver type from constructor calls (`self`/`this` resolution included for all languages) · **Config** — language toolchain config parsing (tsconfig, go.mod, etc.) · **Frameworks** — AST-based framework pattern detection · **Entry Points** — entry point scoring heuristics
 
-**R (experimental)** — `.r` / `.R` files, parsed with `@eagleoutice/tree-sitter-r`. Extracts functions, S4 classes (`setClass`, `setGeneric`, `setMethod`, slots), R6 classes with their methods and fields, R5 (`setRefClass`) methods, and roxygen2 `@param` types. The scope-resolution pipeline resolves `library()` / `require()` / `source()` imports to local packages and files, NAMESPACE `importFrom()` names to local packages, `obj$method()` calls (receiver type inferred from `Type$new()`), calls inside native pipe (`|>`) chains, and R6 `inherit=` / S4 `contains=` heritage. Known limits: a bare call to a function defined in another file of the same package is bound by a workspace-wide unique-name fallback rather than package-namespace lookup; NAMESPACE `export()` is not applied (every top-level symbol is treated as public) and only `importFrom()` is read from NAMESPACE; imports of external (CRAN) packages produce no edges; no framework or entry-point detection.
+**R (experimental)** — `.r` / `.R` files, parsed with `@eagleoutice/tree-sitter-r`. Extracts functions (S3 methods appear as dotted-name functions such as `print.foo`), S4 classes (`setClass`, `setGeneric`, `setMethod`, slots), R6 classes with their methods and fields, R5 (`setRefClass`) methods, and roxygen2 `@param` types. The scope-resolution pipeline resolves `library()` / `require()` / `source()` imports to local packages and files, binds NAMESPACE `importFrom()` names to definitions in local packages, resolves `obj$method()` calls (receiver type inferred from `Type$new()`), follows calls inside native pipe (`|>`) chains, and links R6 `inherit=` / S4 `contains=` heritage. Export status is read from each local package's NAMESPACE (a `DESCRIPTION` marks the package): `export()`, `exportClasses()`, `exportMethods()`, `S3method()` and `exportPattern()` (multi-line directives, R string escapes and POSIX character classes handled) decide which symbols keep `isExported`; the language-level export check treats every symbol as public, and the NAMESPACE pass then marks the rest of a NAMESPACE-bearing package non-exported. Packages without a NAMESPACE stay fully public, and roxygen2 `@export` tags are not consulted. Known limits: a bare call to a function in another file of the same package binds through a workspace-wide unique-name fallback at confidence 0.5 (`global-name-fallback`), not package-namespace lookup, and an ambiguous name yields no edge; dotted (S3-style) names are never import-resolved and bind by qualified-name lookup at 0.35; `pkg::name()` ignores its qualifier; `import()`, `importClassesFrom()` and `importMethodsFrom()` are not read; `exportPattern()` character classes use ASCII semantics; S4 `contains=` links only to classes defined in the repository or the `VIRTUAL` marker, so basic-type bases add no edge; imports of external (CRAN) packages produce no edges; an edit to NAMESPACE alone is not re-resolved by an incremental re-index, so run a full analyze after changing it; no framework or entry-point detection.
 
 **Control flow (CFG, opt-in `--pdg`)** — per-function control-flow graphs (`BasicBlock` nodes + `CFG` edges) feeding the PDG/taint substrate, currently **TypeScript & JavaScript** (#2081 M1); other languages planned. Off by default.
 

gitnexus/README.md

@@ -480,11 +480,11 @@ TypeScript, JavaScript, Python, Java, C, C++, C#, Go, Rust, PHP, Kotlin, Swift,
 | C++        | —       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
 | Dart       | ✓       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
 | Zig        | ✓       | —              | ✓       | —        | ✓                | ✓                     | ✓      | —          | ✓            |
-| R (experimental) | ✓  | ✓              | —       | ✓        | ✓                | ✓                     | ✓      | —          | —            |
+| R (experimental) | ✓  | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | —          | —            |
 
 **Imports** — cross-file import resolution · **Named Bindings** — `import { X as Y }` / re-export tracking · **Exports** — public/exported symbol detection · **Heritage** — class inheritance, interfaces, mixins · **Type Annotations** — explicit type extraction for receiver resolution · **Constructor Inference** — infer receiver type from constructor calls (`self`/`this` resolution included for all languages) · **Config** — language toolchain config parsing (tsconfig, go.mod, etc.) · **Frameworks** — AST-based framework pattern detection · **Entry Points** — entry point scoring heuristics
 
-**R (experimental)** — `.r` / `.R` files, parsed with `@eagleoutice/tree-sitter-r`. Extracts functions, S4 classes (`setClass`, `setGeneric`, `setMethod`, slots), R6 classes with their methods and fields, R5 (`setRefClass`) methods, and roxygen2 `@param` types. The scope-resolution pipeline resolves `library()` / `require()` / `source()` imports to local packages and files, NAMESPACE `importFrom()` names to local packages, `obj$method()` calls (receiver type inferred from `Type$new()`), calls inside native pipe (`|>`) chains, and R6 `inherit=` / S4 `contains=` heritage. Known limits: a bare call to a function defined in another file of the same package is bound by a workspace-wide unique-name fallback rather than package-namespace lookup; NAMESPACE `export()` is not applied (every top-level symbol is treated as public) and only `importFrom()` is read from NAMESPACE; imports of external (CRAN) packages produce no edges; no framework or entry-point detection.
+**R (experimental)** — `.r` / `.R` files, parsed with `@eagleoutice/tree-sitter-r`. Extracts functions (S3 methods appear as dotted-name functions such as `print.foo`), S4 classes (`setClass`, `setGeneric`, `setMethod`, slots), R6 classes with their methods and fields, R5 (`setRefClass`) methods, and roxygen2 `@param` types. The scope-resolution pipeline resolves `library()` / `require()` / `source()` imports to local packages and files, binds NAMESPACE `importFrom()` names to definitions in local packages, resolves `obj$method()` calls (receiver type inferred from `Type$new()`), follows calls inside native pipe (`|>`) chains, and links R6 `inherit=` / S4 `contains=` heritage. Export status is read from each local package's NAMESPACE (a `DESCRIPTION` marks the package): `export()`, `exportClasses()`, `exportMethods()`, `S3method()` and `exportPattern()` (multi-line directives, R string escapes and POSIX character classes handled) decide which symbols keep `isExported`; the language-level export check treats every symbol as public, and the NAMESPACE pass then marks the rest of a NAMESPACE-bearing package non-exported. Packages without a NAMESPACE stay fully public, and roxygen2 `@export` tags are not consulted. Known limits: a bare call to a function in another file of the same package binds through a workspace-wide unique-name fallback at confidence 0.5 (`global-name-fallback`), not package-namespace lookup, and an ambiguous name yields no edge; dotted (S3-style) names are never import-resolved and bind by qualified-name lookup at 0.35; `pkg::name()` ignores its qualifier; `import()`, `importClassesFrom()` and `importMethodsFrom()` are not read; `exportPattern()` character classes use ASCII semantics; S4 `contains=` links only to classes defined in the repository or the `VIRTUAL` marker, so basic-type bases add no edge; imports of external (CRAN) packages produce no edges; an edit to NAMESPACE alone is not re-resolved by an incremental re-index, so run a full analyze after changing it; no framework or entry-point detection.
 
 ## Agent Skills