[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_parser/src/parser/mod.rs

@@ -2,7 +2,7 @@ use std::cmp::Ordering;
 
 use bitflags::bitflags;
 
-use ruff_python_ast::{Mod, ModExpression, ModModule};
+use ruff_python_ast::{AtomicNodeIndex, Mod, ModExpression, ModModule};
 use ruff_text_size::{Ranged, TextRange, TextSize};
 
 use crate::error::UnsupportedSyntaxError;
@@ -132,6 +132,7 @@ impl<'src> Parser<'src> {
         ModExpression {
             body: Box::new(parsed_expr.expr),
             range: self.node_range(start),
+            node_index: AtomicNodeIndex::dummy(),
         }
     }
 
@@ -149,6 +150,7 @@ impl<'src> Parser<'src> {
         ModModule {
             body,
             range: TextRange::new(self.start_offset, self.current_token_range().end()),
+            node_index: AtomicNodeIndex::dummy(),
         }
     }