Harden pipeline state and plan release upgrades

internal/config/load.go

@@ -95,6 +95,7 @@ func LoadPipelineProfilePair(path, leftProfile, rightProfile string) (*PipelineC
 func finalizeLoadedPipeline(path string, cfg *PipelineConfig) (*PipelineConfig, error) {
 	cfg.resolution.publishDeclared = cfg.Publish != nil
 	applyPipelineDefaults(cfg)
+	captureLogicalNotariusPaths(cfg)
 	if err := resolveNotariusPaths(cfg, path); err != nil {
 		return nil, fmt.Errorf("load pipeline config: %w", err)
 	}