Merge Dev - Multi-file support for code optimization

[aliroberts]

Add multi-file optimization support to weco-cli

Summary

• Add --sources flag to optimize multiple files simultaneously
• Simplify internal code handling to work exclusively with dict[str, str] file maps
• Update README with multi-file usage and examples

Changes

New --sources flag

Added --sources as a mutually exclusive alternative to -s/--source:

# Single file (existing)
weco run -s model.py -c "python eval.py" -m accuracy -g maximize

# Multiple files (new)
weco run --sources model.py utils.py config.py -c "python eval.py" -m accuracy -g maximize

Accepts one or more file paths via nargs="+". Internally, both flags normalize to the same list[str] passed to the optimizer.

Simplified code handling

The server now always returns code as dict[str, str] to new CLI versions. Removed isinstance branching in:

• Execution loop (optimizer.py): code from the server is always a dict file map — removed the string-to-dict conversion branch
• Best solution handler (optimizer.py): best_code is always a dict — removed string branch, always iterates file map to write each file to disk
• Resume handler (optimizer.py): resume_source_code from server is always a dict — removed source_path/scoped_files fallback branches

API signature

source_code parameter in api.py changed from str | dict[str, str] to dict[str, str].

Validation

Source validation (validation.py) updated to accept list[str] and validate all paths exist and are readable.

README

• Added --sources to the required arguments table (mutually exclusive with -s/--source)
• Added multi-file usage example
• Updated evaluation note to reference both flags