Unify CLI configuration selection and overrides
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@@ -147,7 +147,15 @@ Do not duplicate ConfigKit's exhaustive YAML/merge tests.
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## Stage 2: Replace CLI Configuration Selection and Overrides
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**Status:** Pending. **Depends on:** Stage 1.
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**Status:** Complete (2026-09-24). Added one parser for all three commands,
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strict file discovery, optional overlay selection, and visited-only setting
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overrides; removed retired flags and legacy process flag extraction. Updated CLI
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and configuration references. Isolated parser/loading tests passed with
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`go test internal/cli/config_input.go internal/cli/config_input_test.go`, and
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`git diff --check` passed. `go test ./internal/cli` remains unbuildable because
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the old runtime, validators, and diagnostics still use removed configuration
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fields; assembled command checks remain deferred to later stages.
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**Depends on:** Stage 1.
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**Owns:** `internal/cli/run.go`, `process_flags.go`, configuration command parsing,
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and corresponding CLI/subprocess tests.
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