Update cli to handle multi-file optimization

[aliroberts]

Multi-file optimization support

Extends the CLI to optimize across multiple source files in a single run, while remaining fully backwards-compatible with the existing single-file (-s/--source) workflow.

Changes

CLI (cli.py)

• Add --sources flag (mutually exclusive with -s/--source) accepting multiple file paths.
• Normalize both input modes into a unified list[str] before passing downstream.

Optimizer (optimizer.py)

• Represent source code as dict[str, str] (path -> content) throughout the optimization loop and resume flow.
• Normalize server responses (single string or dict) into a file map at every boundary.
• Replace inline log-writing with the new RunArtifacts manager.
• Multi-file apply: _offer_apply_best_solution writes back all modified files and displays which paths changed.

Artifacts (artifacts.py) — new

• RunArtifacts class that owns the on-disk layout under .runs/<run_id>/.
• Step snapshots (steps/<n>/files/ + manifest.json), best snapshot (best/), and execution output (outputs/ + exec_output.jsonl).
• Path sanitization (_sanitize_artifact_path) strips traversal components, absolute prefixes, and Windows drive letters.

Utils (utils.py)

• Add run_evaluation_with_files_swap() — atomically swaps multiple files before evaluation and restores originals in a finally block.

Validation (validation.py)

• Add validate_source_files() with per-file size (200 KB), total size (500 KB), file count (10), and duplicate-path checks.
• Add validate_sources() dispatcher that routes single vs. multi-file input.

API (api.py)

• Widen start_optimization_run signature: source_code accepts str | dict[str, str], source_path accepts str | None.

Tests (test_artifacts.py) — new

• Parametrized path-sanitization tests (relative, absolute, traversal, Windows, empty).
• Step/best snapshot round-trip tests, step independence, JSONL index verification.
• Path-traversal containment tests for both step and best snapshots.