update file formats section

docs/file_formats.md

@@ -253,6 +253,6 @@ Similarly, in Casanovo evaluation mode only annotated MGF files are supported.
 <!-- TODO: when index files can be reused, document this here -->
 
 During training, Casanovo will save **checkpoint files** at every `val_check_interval` steps, specified in the configuration.
-Model checkpoints will be saved in the `model_save_folder_path` folder with filename format `epoch=EPOCH-step=STEP.ckpt`, with `EPOCH` the epoch and `STEP` the training step at which the checkpoint was taken, helping you track progress and select the best model based on validation performance.
+Model checkpoints will be saved to the folder specified by the `--output_dir` command line option with filename format `epoch=EPOCH-step=STEP.ckpt`, with `EPOCH` the epoch and `STEP` the training step at which the checkpoint was taken, helping you track progress and select the best model based on validation performance.
 
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