fix[docs]: update references in vyper/ast/README.md

[GarmashAlex]

Update README.md to reflect current file structure in vyper/ast module

• Replace references to non-existent annotation.py with parse.py
• Update documentation to point to correct location of AnnotatingVisitor class
• Fix broken file links in module organization section

The AnnotatingVisitor class was moved from annotation.py to parse.py but the
documentation was not updated accordingly, causing broken references.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.06%. Comparing base (90c952c) to head (bf6c2a3).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #4731   +/-   ##
=======================================
  Coverage   93.06%   93.06%           
=======================================
  Files         131      131           
  Lines       19134    19134           
  Branches     3323     3323           
=======================================
  Hits        17807    17807           
  Misses        894      894           
  Partials      433      433           

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