fix: preserve repeated add-dir flags in claude args

[Jerry2003826]

Fixes #1215

Summary

• Preserve repeated --add-dir flags parsed from claude_args.
• Map parsed directory values onto the SDK's typed additionalDirectories option.
• Remove add-dir from extraArgs so the SDK does not receive a single overwritten or delimiter-joined value.

Root Cause

parseClaudeArgsToExtraArgs() stores CLI flags in a record keyed by flag name. Since add-dir was not treated as an accumulating flag, repeated values overwrote earlier directories before reaching the SDK.

Validation

• bun test test/parse-sdk-options.test.ts -t add-dir
• bun test test/parse-sdk-options.test.ts
• bun test
• bun run typecheck
• bunx prettier --check src/parse-sdk-options.ts test/parse-sdk-options.test.ts