feat: add pipeline orchestration with incremental analysis, optimized…

[shrutu0929]

solve #177
This task introduced a robust timing and session persistence layer to the Refactron pipeline, enabling precise duration tracking across critical orchestration phases. By implementing a new PipelineSession core model, the system now captures high-resolution metrics for the analysis, queuing, application, and verification stages, providing operators with immediate visibility into pipeline efficiency. These metrics are exposed through an enhanced refactron run command via a new --verbose flag and a dedicated debug mode, allowing for granular bottleneck identification in both local and CI/CD environments. The implementation is fully verified with a dedicated unit test suite ensuring session serializability and timing accuracy, and it includes a project-wide configuration fix to ensure seamless integration with the updated instrumentation.

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⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 0366b30d-8775-4cff-bfd1-44af86ddea6d

📥 Commits

Reviewing files that changed from the base of the PR and between a9659f5 and b987aa9.

📒 Files selected for processing (7)

• .refactron.yaml
• refactron/cli/main.py
• refactron/cli/run.py
• refactron/core/pipeline.py
• refactron/core/pipeline_session.py
• tests/test_pipeline.py
• tests/test_pipeline_session.py

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