Possible re-factor to make more central use of the pipeline graph

ceci/pipeline/__init__.py

@@ -11,5 +11,5 @@
 from .dry_run import DryRunPipeline
 from .flow_chart import FlowChartPipeline
 from .mini import MiniPipeline
-from .file_manager import FileManager
 from .sec import StageExecutionConfig
+from .graph import StageStatus

ceci/pipeline/dry_run.py

@@ -18,11 +18,11 @@ def initiate_run(self, overall_inputs):
     def should_skip_stage(self, stage):
         return False
 
-    def enqueue_job(self, stage, pipeline_files):
+    def enqueue_job(self, stage, input_paths):
         outputs = stage.find_outputs(self.run_config["output_dir"])
-        sec = self.stage_execution_config[stage.instance_name]
+        sec = self.get_stage_execution_config(stage.instance_name)
 
-        cmd = sec.generate_full_command(pipeline_files, outputs, self.stages_config)
+        cmd = sec.generate_full_command(input_paths, outputs, self.stages_config)
 
         # Replace the first instance of the stage name with bold
         # text, but only if we are printing to screen. This helps the