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fix(path): fix subdirectory path issues (#1298)
* Checking for model_relative_path already existing in external file filename, which will be the case when reading in a model. Will only append model_relative_path where not already present in file name. Should improve support for models using external file storage and simulations with models in sub directories. * Added test to t501 to catch subdir issue * Close #1289 * Possibly related to #1115 and #1126
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