Override files were resolved late, in the emit_template stage, so they
did not apply to file-existence validation nor to the slang file-list
reduction. This meant a shadowed original still had to exist on disk,
and slang parsed both the original and its override as duplicate module
definitions.

Resolve override_files right after flatten() instead: drop the override
groups and rewrite like-named files in the regular groups to the
overriding path (preserving SourceType). Only the overriding files are
then validated, and slang analyzes/reduces them instead of the files
they shadow. The OVERRIDDEN annotation is carried through a side map so
--source-annotations output is unchanged.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>