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feat: enhance analysis capabilities and add comprehensive test projects
- Enhanced Java analysis module with modern feature detection, collection factory analysis, and performance metrics - Significantly expanded Python user model with design patterns (observer, singleton, builder, factory, strategy) - Added comprehensive test projects for Java, Rust, and additional JavaScript components - Added MCP test harness documentation and verification checklist - Included test files for duplicate code detection and unused code analysis - Removed outdated milestone reports (MILESTONE_3_ACTUAL_STATUS_REPORT.md, MILESTONE_3_QA_REPORT.md) All tests passing (583 tests: 582 passed, 1 ignored). Build successful.
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