feat: persist pipeline phase timings on PipelineSession

[omsherikar]

Summary

End-to-end orchestration (analyze → queue → fix → verify) lacks first-class timing in PipelineSession. Operators cannot see whether slowness is analysis, fixer matching, verification, or I/O without parsing logs.

Suggested direction

• Add optional fields e.g. analyze_ms, queue_ms, apply_ms, verify_ms (or nested timings: dict) populated on the session.
• Emit the same summary in CLI for refactron run when --verbose or REFACTRON_DEBUG.

Acceptance

• Session JSON remains backward compatible (new optional fields).
• Tests cover that timings are non-negative and set when phases run.

Code

• refactron/core/pipeline_session.py — PipelineSession
• refactron/core/pipeline.py — analyze, queue_issues, apply
• refactron/cli/run.py