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feat(phase4): Fragment Salvage + Refinement + run_thoughtforge CLI #5

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Run time

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Job	Run time
Lint (ruff + mypy)	1m 34s
Tests (Python 3.10)	2m 15s
Tests (Python 3.12)	1m 49s
Tests (Python 3.11)	1m 44s
Tests (Python 3.12)	2m 31s
Tests (Python 3.12)	1m 3s
Tests (Python 3.10)	1m 37s
Tests (Python 3.11)	1m 1s
Tests (Python 3.10)	1m 25s
Tests (Python 3.11)	2m 35s
	17m 34s