Fix bare script variable scoping

[JesseHerrick]

The Problem: Go to definition wasn't working for variables in the top level of an exs script.

Solution: Properly handle this case.

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Note

Medium Risk
Changes core rename/go-to-definition scoping and parser index references; incorrect boundaries could mis-rename or miss symbols, mitigated by extensive new tests and an index version bump.

Overview
Fixes variable scoping for bare .exs scripts (e.g. config/runtime.exs) so top-level bindings are treated as file-scoped, while nested def/defmodule bodies stay isolated for rename, occurrence collection, and collision checks.

In internal/treesitter/variables.go, scope discovery now stops at the source root and at defmodule/defprotocol/defimpl calls; traversals skip nested function and module definitions so same-named locals do not leak across boundaries. Bare top-level identifiers that are only zero-arity calls are not misclassified as variables when a same-named binding exists inside a nested def.

The tokenized parser resolves import / use / require module names via ResolveModuleRef (aliases + current module) instead of plain resolveModule, improving indexing in scripts without an enclosing module.

Adds LSP rename coverage for plain alias + require short name in the same config file, plus tree-sitter tests for top-level and cross-boundary cases. IndexVersion is bumped to 12 for index rebuilds.

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