Add scalable project-wide R indexing

[renkun-ken]

Summary

• index complete R projects with a scalable two-tier strategy
• shallow-index unrelated scripts while fully parsing package files, open files, and transitive static source() dependencies
• isolate unrelated scripts from semantic features and support exclusions, limits, batching, caching, cycles, watcher invalidation, nested packages, and runtime configuration
• integrate the project index across completion, hover, signature help, definitions, references, hierarchies, code lenses, diagnostics, and inlay hints

Issues

• Fixes Extend completion with source by recursive parsing #20 — recursively parse static source() dependency closures for context-aware completion and language features
• Fixes Support dir-nested R packages (monorepo support) #619 — discover nested package roots independently within a workspace
• Partially addresses language server should be able to fufill requests even without textdocument/didOpen Notifications #15, Go to definition in another file #253, and Configurable source dirs for file parsing #386 by indexing closed project files, exposing workspace symbols, and adding configurable include/exclude globs. Unrelated one-off scripts remain isolated from semantic definition/reference scopes unless they are open, package files, or statically source-linked.

Testing

• GitHub Actions lint
• GitHub Actions R CMD check on Ubuntu, macOS, and Windows
• GitHub Actions test coverage
• installed-package end-to-end indexing tests
• focused completion, hover, signature, definition, references, call/type hierarchy, code-lens, inlay-hint, handler, and index tests
• git diff --check