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Replace environment variable communication between cmd and internal
packages with explicit MCPOverrides struct. CLI flag values are now
passed via typed struct fields through Run/RunWithFactory/RunBackfill.
Env var support preserved through appconfig's applyMCPEnv pipeline.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Change initDebugLog() and defaultLogPath() to return errors instead of
panicking. Callers now handle errors gracefully with proper messages.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Bring unit test coverage from ~75% to 85.1% project-wide. All internal
packages now exceed 80% coverage. Refactored cmd entrypoints to extract
testable run() functions with injectable seams.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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