[ty] AST garbage collection (#18482)

## Summary

Garbage collect ASTs once we are done checking a given file. Queries
with a cross-file dependency on the AST will reparse the file on demand.
This reduces ty's peak memory usage by ~20-30%.

The primary change of this PR is adding a `node_index` field to every
AST node, that is assigned by the parser. `ParsedModule` can use this to
create a flat index of AST nodes any time the file is parsed (or
reparsed). This allows `AstNodeRef` to simply index into the current
instance of the `ParsedModule`, instead of storing a pointer directly.

The indices are somewhat hackily (using an atomic integer) assigned by
the `parsed_module` query instead of by the parser directly. Assigning
the indices in source-order in the (recursive) parser turns out to be
difficult, and collecting the nodes during semantic indexing is
impossible as `SemanticIndex` does not hold onto a specific
`ParsedModuleRef`, which the pointers in the flat AST are tied to. This
means that we have to do an extra AST traversal to assign and collect
the nodes into a flat index, but the small performance impact (~3% on
cold runs) seems worth it for the memory savings.

Part of https://github.com/astral-sh/ty/issues/214.

crates/ruff_python_formatter/src/module/mod_expression.rs

@@ -7,7 +7,11 @@ pub struct FormatModExpression;
 
 impl FormatNodeRule<ModExpression> for FormatModExpression {
     fn fmt_fields(&self, item: &ModExpression, f: &mut PyFormatter) -> FormatResult<()> {
-        let ModExpression { body, range: _ } = item;
+        let ModExpression {
+            body,
+            range: _,
+            node_index: _,
+        } = item;
         body.format().fmt(f)
     }
 }

crates/ruff_python_formatter/src/module/mod_module.rs

@@ -11,7 +11,11 @@ pub struct FormatModModule;
 
 impl FormatNodeRule<ModModule> for FormatModModule {
     fn fmt_fields(&self, item: &ModModule, f: &mut PyFormatter) -> FormatResult<()> {
-        let ModModule { range, body } = item;
+        let ModModule {
+            range,
+            body,
+            node_index: _,
+        } = item;
 
         if body.is_empty() {
             // Only preserve an empty line if the source contains an empty line too.