diff --git a/examples/DSPC_custom_XY/project.json b/examples/DSPC_custom_XY/project.json
index 26ce9898..e14f45d6 100644
--- a/examples/DSPC_custom_XY/project.json
+++ b/examples/DSPC_custom_XY/project.json
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/examples/DSPC_custom_layers/project.json b/examples/DSPC_custom_layers/project.json
index 1d0100a0..4b54aca7 100644
--- a/examples/DSPC_custom_layers/project.json
+++ b/examples/DSPC_custom_layers/project.json
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/examples/DSPC_standard_layers/project.json b/examples/DSPC_standard_layers/project.json
index 64069a40..32186916 100644
--- a/examples/DSPC_standard_layers/project.json
+++ b/examples/DSPC_standard_layers/project.json
@@ -1 +1 @@
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\ No newline at end of file
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out"}, {"name": "SAM Heads", "thickness": "SAM Heads Thickness", "SLD": "SAM Heads SLD", "roughness": "SAM Roughness", "hydration": "SAM Heads Hydration", "hydrate_with": "bulk out"}, {"name": "Central Water", "thickness": "CW Thickness", "SLD": "CW SLD", "roughness": "Bilayer Roughness", "hydration": "CW Hydration", "hydrate_with": "bulk out"}, {"name": "Bilayer Heads", "thickness": "Bilayer Heads Thickness", "SLD": "Bilayer Heads SLD", "roughness": "Bilayer Roughness", "hydration": "Bilayer Heads Hydration", "hydrate_with": "bulk out"}, {"name": "Bilayer Tails", "thickness": "Bilayer Tails Thickness", "SLD": "Bilayer Tails SLD", "roughness": "Bilayer Roughness", "hydration": "Bilayer Tails Hydration", "hydrate_with": "bulk out"}], "domain_contrasts": [], "contrasts": [{"name": "D2O", "data": "dspc_bil_D2O", "background": "D2O Background", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": 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\ No newline at end of file
diff --git a/examples/absorption/project.json b/examples/absorption/project.json
index 49ad5020..e123b089 100644
--- a/examples/absorption/project.json
+++ b/examples/absorption/project.json
@@ -1 +1 @@
-{"name": "Absorption example", "calculation": "normal", "model": "custom layers", "geometry": "substrate/liquid", "absorption": true, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Thickness", "min": 100.0, "value": 135.6, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD up", "min": 6e-06, "value": 9.87e-06, "max": 1.2e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD imaginary up", "min": 1e-09, "value": 4.87e-08, "max": 1e-07, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD down", "min": 6e-06, "value": 7.05e-06, "max": 1.3e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD 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\ No newline at end of file
diff --git a/examples/domains_custom_XY/project.json b/examples/domains_custom_XY/project.json
index 3c32479c..bd15ab06 100644
--- a/examples/domains_custom_XY/project.json
+++ b/examples/domains_custom_XY/project.json
@@ -1 +1 @@
-{"name": "", "calculation": "domains", "model": "custom xy", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Oxide Thickness", "min": 10.0, "value": 20.0, "max": 50.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer Thickness", "min": 1.0, "value": 30.0, "max": 500.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer SLD", "min": -5e-07, "value": -5e-07, "max": 0.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer Roughness", "min": 2.0, "value": 5.0, "max": 7.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Domain SLD", "min": 1e-06, "value": 1e-06, "max": 5e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 0.0, "value": 2.073e-06, "max": 1.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SLD SMW", "min": 2e-06, "value": 2.073e-06, "max": 2.1e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SLD H2O", "min": -6e-07, "value": -5.6e-07, "max": -5e-07, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.8, "value": 1.0, "max": 1.1, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "resolution_parameters": [{"name": "Resolution Param 1", "min": 0.01, "value": 0.03, "max": 0.05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "resolutions": [{"name": "Resolution 1", "type": "constant", "source": "Resolution Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "custom_files": [{"name": "Domain Layer", "filename": "domains_XY_model.py", "language": "python", "path": ".", "function_name": "domains_XY_model"}], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [], "domain_contrasts": [], "contrasts": [{"name": "D2O", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}, {"name": "SMW", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD SMW", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}, {"name": "H2O", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD H2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}]}
\ No newline at end of file
+{"name": "Domain Custom XY", "calculation": "domains", "model": "custom xy", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Oxide Thickness", "min": 10.0, "value": 20.0, "max": 50.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer Thickness", "min": 1.0, "value": 30.0, "max": 500.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer SLD", "min": -5e-07, "value": -5e-07, "max": 0.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer Roughness", "min": 2.0, "value": 5.0, "max": 7.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Domain SLD", "min": 1e-06, "value": 1e-06, "max": 5e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 0.0, "value": 2.073e-06, "max": 1.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SLD SMW", "min": 2e-06, "value": 2.073e-06, "max": 2.1e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SLD H2O", "min": -6e-07, "value": -5.6e-07, "max": -5e-07, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.8, "value": 1.0, "max": 1.1, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "resolution_parameters": [{"name": "Resolution Param 1", "min": 0.01, "value": 0.03, "max": 0.05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "resolutions": [{"name": "Resolution 1", "type": "constant", "source": "Resolution Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "custom_files": [{"name": "Domain Layer", "filename": "domains_XY_model.py", "language": "python", "path": ".", "function_name": "domains_XY_model"}], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [], "domain_contrasts": [], "contrasts": [{"name": "D2O", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}, {"name": "SMW", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD SMW", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}, {"name": "H2O", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD H2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}]}
\ No newline at end of file
diff --git a/examples/domains_custom_layers/project.json b/examples/domains_custom_layers/project.json
index db9115ec..3d751d88 100644
--- a/examples/domains_custom_layers/project.json
+++ b/examples/domains_custom_layers/project.json
@@ -1 +1 @@
-{"name": "", "calculation": "domains", "model": "custom layers", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Thickness", "min": 100.0, "value": 150.0, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD up", "min": 9e-06, "value": 1.1e-05, "max": 1.3e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD down", "min": 5e-06, "value": 7e-06, "max": 1e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Roughness", "min": 5.0, "value": 7.0, "max": 11.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold Thickness", "min": 100.0, "value": 150.0, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold SLD", "min": 4e-06, "value": 4.5e-06, "max": 5e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold Roughness", "min": 5.0, "value": 7.0, "max": 11.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 0.0, "value": 2.073e-06, "max": 1.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.02, "value": 0.23, "max": 0.25, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "resolution_parameters": [{"name": "Resolution Param 1", "min": 0.01, "value": 0.03, "max": 0.05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "resolutions": [{"name": "Resolution 1", "type": "constant", "source": "Resolution Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "custom_files": [{"name": "Alloy domains", "filename": "alloy_domains.py", "language": "python", "path": ".", "function_name": "alloy_domains"}], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [], "domain_contrasts": [], "contrasts": [{"name": "D2O Contrast", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": false, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Alloy domains"]}]}
\ No newline at end of file
+{"name": "Domain Custom Layers", "calculation": "domains", "model": "custom layers", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Thickness", "min": 100.0, "value": 150.0, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD up", "min": 9e-06, "value": 1.1e-05, "max": 1.3e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD down", "min": 5e-06, "value": 7e-06, "max": 1e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Roughness", "min": 5.0, "value": 7.0, "max": 11.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold Thickness", "min": 100.0, "value": 150.0, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold SLD", "min": 4e-06, "value": 4.5e-06, "max": 5e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold Roughness", "min": 5.0, "value": 7.0, "max": 11.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 0.0, "value": 2.073e-06, "max": 1.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.02, "value": 0.23, "max": 0.25, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "resolution_parameters": [{"name": "Resolution Param 1", "min": 0.01, "value": 0.03, "max": 0.05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "resolutions": [{"name": "Resolution 1", "type": "constant", "source": "Resolution Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "custom_files": [{"name": "Alloy domains", "filename": "alloy_domains.py", "language": "python", "path": ".", "function_name": "alloy_domains"}], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [], "domain_contrasts": [], "contrasts": [{"name": "D2O Contrast", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": false, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Alloy domains"]}]}
\ No newline at end of file
diff --git a/examples/domains_standard_layers/project.json b/examples/domains_standard_layers/project.json
index 2a579aad..4e62cc80 100644
--- a/examples/domains_standard_layers/project.json
+++ b/examples/domains_standard_layers/project.json
@@ -1 +1 @@
-{"name": "", "calculation": "domains", "model": "standard layers", "geometry": "air/substrate", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L1 Thickness", "min": 5.0, "value": 20.0, "max": 60.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L1 SLD", "min": 3e-06, "value": 4.1e-06, "max": 5e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L1 Roughness", "min": 2.0, "value": 5.0, "max": 20.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L1 Hydration", "min": 10.0, "value": 20.0, "max": 30.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L2 Thickness", "min": 5.0, "value": 60.0, "max": 100.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L2 SLD", "min": 2.1e-06, "value": 3e-06, "max": 5e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L2 Roughness", "min": 2.0, "value": 5.0, "max": 20.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L2 Hydration", "min": 10.0, "value": 20.0, "max": 30.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L3 Thickness", "min": 5.0, "value": 200.0, "max": 300.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L3 SLD", "min": 3e-06, "value": 7e-06, "max": 8e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L3 Roughness", "min": 2.0, "value": 5.0, "max": 20.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L3 Hydration", "min": 10.0, "value": 20.0, "max": 30.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "SLD Air", "min": 0.0, "value": 0.0, "max": 0.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.02, "value": 0.23, "max": 0.25, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "resolution_parameters": [{"name": "Resolution Param 1", "min": 0.01, "value": 0.03, "max": 0.05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "resolutions": [{"name": "Resolution 1", "type": "constant", "source": "Resolution Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "custom_files": [], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [{"name": "Layer 1", "thickness": "L1 Thickness", "SLD": "L1 SLD", "roughness": "L1 Roughness", "hydration": "L1 Hydration", "hydrate_with": "bulk out"}, {"name": "Layer 2", "thickness": "L2 Thickness", "SLD": "L2 SLD", "roughness": "L2 Roughness", "hydration": "L2 Hydration", "hydrate_with": "bulk out"}, {"name": "Layer 3", "thickness": "L3 Thickness", "SLD": "L3 SLD", "roughness": "L3 Roughness", "hydration": "L3 Hydration", "hydrate_with": "bulk out"}], "domain_contrasts": [{"name": "Domain 1", "model": ["Layer 1"]}, {"name": "Domain 2", "model": ["Layer 2", "Layer 3"]}], "contrasts": [{"name": "Domain Test", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "SLD Air", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": false, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain 1", "Domain 2"]}]}
\ No newline at end of file
+{"name": "Domain Standard Layers", "calculation": "domains", "model": "standard layers", "geometry": "air/substrate", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L1 Thickness", "min": 5.0, "value": 20.0, "max": 60.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L1 SLD", "min": 3e-06, "value": 4.1e-06, "max": 5e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L1 Roughness", "min": 2.0, "value": 5.0, "max": 20.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L1 Hydration", "min": 10.0, "value": 20.0, "max": 30.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L2 Thickness", "min": 5.0, "value": 60.0, "max": 100.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L2 SLD", "min": 2.1e-06, "value": 3e-06, "max": 5e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L2 Roughness", "min": 2.0, "value": 5.0, "max": 20.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L2 Hydration", "min": 10.0, "value": 20.0, "max": 30.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L3 Thickness", "min": 5.0, "value": 200.0, "max": 300.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L3 SLD", "min": 3e-06, "value": 7e-06, "max": 8e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L3 Roughness", "min": 2.0, "value": 5.0, "max": 20.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "L3 Hydration", "min": 10.0, "value": 20.0, "max": 30.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "SLD Air", "min": 0.0, "value": 0.0, "max": 0.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.02, "value": 0.23, "max": 0.25, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "resolution_parameters": [{"name": "Resolution Param 1", "min": 0.01, "value": 0.03, "max": 0.05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "resolutions": [{"name": "Resolution 1", "type": "constant", "source": "Resolution Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "custom_files": [], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [{"name": "Layer 1", "thickness": "L1 Thickness", "SLD": "L1 SLD", "roughness": "L1 Roughness", "hydration": "L1 Hydration", "hydrate_with": "bulk out"}, {"name": "Layer 2", "thickness": "L2 Thickness", "SLD": "L2 SLD", "roughness": "L2 Roughness", "hydration": "L2 Hydration", "hydrate_with": "bulk out"}, {"name": "Layer 3", "thickness": "L3 Thickness", "SLD": "L3 SLD", "roughness": "L3 Roughness", "hydration": "L3 Hydration", "hydrate_with": "bulk out"}], "domain_contrasts": [{"name": "Domain 1", "model": ["Layer 1"]}, {"name": "Domain 2", "model": ["Layer 2", "Layer 3"]}], "contrasts": [{"name": "Domain Test", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "SLD Air", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": false, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain 1", "Domain 2"]}]}
\ No newline at end of file
diff --git a/rascal2/config.py b/rascal2/config.py
index 184c5aab..71becea1 100644
--- a/rascal2/config.py
+++ b/rascal2/config.py
@@ -8,7 +8,7 @@
 import site
 import sys
 
-from rascal2.settings import get_global_settings
+from rascal2.settings import Settings, get_global_settings
 
 if getattr(sys, "frozen", False):
     # we are running in a bundle
@@ -28,6 +28,7 @@
 MATLAB_ARCH_FILE = pathlib.Path(SITE_PATH) / "matlab/engine/_arch.txt"
 EXAMPLES_TEMP_PATH = pathlib.Path(get_global_settings().fileName()).parent / "examples"
 LOGGER = logging.getLogger("rascal2")
+SETTINGS = Settings()
 
 
 def handle_scaling():
diff --git a/rascal2/core/commands.py b/rascal2/core/commands.py
index 2f712e61..532908d5 100644
--- a/rascal2/core/commands.py
+++ b/rascal2/core/commands.py
@@ -68,7 +68,7 @@ def redo(self):
                 try:
                     self.new_result = self.presenter.quick_run()
                 except Exception as ex:
-                    self.new_result = self.old_result
+                    self.new_result = None
                     message = f"Error occurred when generating result preview:\n\n{ex}"
                     LOGGER.error(message, exc_info=ex)
                     self.presenter.view.terminal_widget.write(message)
diff --git a/rascal2/core/enums.py b/rascal2/core/enums.py
index c485f776..30c1cf49 100644
--- a/rascal2/core/enums.py
+++ b/rascal2/core/enums.py
@@ -10,3 +10,10 @@ class UnsavedReply(StrEnum):
     Save = "Save"
     Discard = "Discard"
     Cancel = "Cancel"
+
+
+class CustomFileType(StrEnum):
+    """The responses to the warning of unsaved changes."""
+
+    Background = "Background"
+    Model = "Model"
diff --git a/rascal2/core/runner.py b/rascal2/core/runner.py
index 602f9899..7e18f2cf 100644
--- a/rascal2/core/runner.py
+++ b/rascal2/core/runner.py
@@ -1,5 +1,6 @@
 """QObject for running rat."""
 
+import os
 from dataclasses import dataclass
 from logging import INFO
 from multiprocessing import Process, Queue
@@ -105,6 +106,7 @@ def run(queue, rat_inputs: tuple, procedure: str, display: bool, engine_ready, e
                 raise result
             else:
                 engine_future = result
+                engine_future.result().cd(os.getcwd())
 
         problem_definition, output_results, bayes_results = rat.rat_core.RATMain(problem_definition, cpp_controls)
         results = rat.outputs.make_results(procedure, output_results, bayes_results)
diff --git a/rascal2/dialogs/custom_file_editor.py b/rascal2/dialogs/custom_file_editor.py
index eea963bf..2b895cc6 100644
--- a/rascal2/dialogs/custom_file_editor.py
+++ b/rascal2/dialogs/custom_file_editor.py
@@ -1,15 +1,159 @@
 """Dialogs for editing custom files."""
 
+import os
+import re
 from pathlib import Path
 
 from PyQt6 import Qsci, QtGui, QtWidgets
 from ratapi.utils.enums import Languages
 
-from rascal2.config import EXAMPLES_PATH, LOGGER, MatlabHelper
+from rascal2.config import EXAMPLES_PATH, LOGGER, SETTINGS, MatlabHelper
+from rascal2.core.enums import CustomFileType
+
+MATLAB_MODEL_TEMPLATE = """function [output, sub_rough] = {0}{1}
+% RasCAL-2 Layer Model Custom File.
+%
+% The first 3 arguments are vectors containing the values for parameters, bulk in and bulk out
+% The fourth argument is a number indicating which contrast is being calculated (this number starts from 1)
+% {2}
+% This function should return an array of layer values in the form:
+% output = [Thickness 1, SLD 1, Roughness 1, Percent Hydration 1, Hydrate how 1;
+%           ....
+%           Thickness n, SLD n, Roughness n, Percent Hydration n, Hydrate how n]
+% The "Hydrate how" parameter decides if the layer is hydrated with
+% Bulk in or Bulk out phases. Set to 0 for Bulk in or 1 for Bulk out.
+% Alternatively, leave out hydration and just return:
+% output = [Thickness 1, SLD 1, Roughness 1;
+%           ....
+%           Thickness n, SLD n, Roughness n];
+% The second output parameter should be the substrate roughness."""
+
+
+PYTHON_MODEL_TEMPLATE = """def {0}{1}:
+    \"\"\"RasCAL-2 Layer Model Custom File.
+    
+    The first 3 arguments are vectors containing the values for parameters, bulk in and bulk out
+    The fourth argument is a number indicating which contrast is being calculated (this number starts from 1)
+    {2}
+    This function should return a tuple with 2 entries. The first entry is an array of layer values in the form:
+    output = [[Thickness 1, SLD 1, Roughness 1, Percent Hydration 1, Hydrate how 1],
+               ....
+              [Thickness n, SLD n, Roughness n, Percent Hydration n, Hydrate how n]]
+    The "Hydrate how" parameter decides if the layer is hydrated with
+    Bulk in or Bulk out phases. Set to 0 for Bulk in or 1 for Bulk out.
+    Alternatively, leave out hydration and just return:
+    output = [[Thickness 1, SLD 1, Roughness 1]
+               ....
+              [Thickness n, SLD n, Roughness n]]
+    The second output parameter should be the substrate roughness.\"\"\"
+"""
+
+
+PYTHON_BACKGROUND_TEMPLATE = """def {0}(xdata, params):
+    \"\"\"RasCAL-2 Background Custom File.
+    
+    The first argument is a vector containing the q points over the simulation range, which should incorporate 
+    the q values of the supplied data.
+    The second argument is a vector containing the background parameters associated with the background.
+    
+    This function should return an array with the background value for each of the input simulation points.\"\"\"
+"""
+
+
+MATLAB_BACKGROUND_TEMPLATE = """function background = {0}(xdata, params)
+% RasCAL-2 Background Custom File.
+%
+% The first argument is a vector containing the q points over the simulation range, which should incorporate 
+% the q values of the supplied data.
+% The second argument is a vector containing the background parameters associated with the background.
+%
+% This function should return an array with the background value for each of the input simulation points."""
+
+
+def create_new_file(
+    name: str, language: Languages, is_domains: bool, file_type: CustomFileType, parent: QtWidgets.QWidget
+):
+    """Create a new file using a template and opens the file in the editor.
+
+    Parameters
+    ----------
+    name : str
+        The unique name used to generate filename.
+    language : str
+        The language of file
+    is_domains : str
+        Indicates if the file is for domains project.
+    file_type : CustomFileType
+        The type of custom file i.e. model or background.
+    parent : str
+        The parent of editor widget.
+
+    Returns
+    -------
+    filename: str
+        The path of the new custom file.
+    """
+    # remove symbols from name since this will be used for file and function name
+    name = re.sub(r"[^\w]", "", name.replace(" ", "_"))
+    function_name = name.lower()
+    if language == Languages.Python:
+        ext = ".py"
+        comment = PYTHON_MODEL_TEMPLATE if file_type == CustomFileType.Model else PYTHON_BACKGROUND_TEMPLATE
+        signature = "(params, bulk_in, bulk_out, contrast{0})"
+    elif language == Languages.Matlab:
+        ext = ".m"
+        comment = MATLAB_MODEL_TEMPLATE if file_type == CustomFileType.Model else MATLAB_BACKGROUND_TEMPLATE
+        signature = "(params, bulkIn, bulkOut, contrast{0})"
+    else:
+        LOGGER.error(f"Creating a new file for {language} is not supported.")
+        return
+
+    filename = f"{function_name}{ext}"
+    if file_type == CustomFileType.Model:
+        signature = signature.format(", domain" if is_domains else "")
+        extra = (
+            "The fifth argument is a number indicating which domain is being calculated (this number starts from 1).\n"
+            if is_domains
+            else ""
+        )
+        comment = comment.format(function_name, signature, extra)
+    else:
+        comment = comment.format(function_name)
+
+    if Path(filename).is_file():
+        LOGGER.error(f"The file ({filename}) already exists, change custom file name to create a different file.")
+        return
+
+    with open(filename, "w") as f:
+        f.write(comment)
+
+    edit_file(filename, language, parent)
+    return filename
 
 
 def edit_file(filename: str, language: Languages, parent: QtWidgets.QWidget):
-    """Edit a file in the file editor.
+    """Edit a file in the user's default file editor.
+
+    Parameters
+    ----------
+    filename : str
+        The name of the file to edit.
+    language : Languages
+        The language for dialog highlighting.
+    parent : QtWidgets.QWidget
+        The parent of this widget.
+
+    """
+    use_matlab = SETTINGS.matlab_as_default_editor or language == Languages.Matlab
+    if use_matlab and edit_file_matlab(filename):
+        return
+
+    # Always fallback to RasCAL editor if MATLAB is not available
+    edit_file_local(filename, language, parent)
+
+
+def edit_file_local(filename: str, language: Languages, parent: QtWidgets.QWidget):
+    """Edit a file in the RasCAL file editor.
 
     Parameters
     ----------
@@ -38,9 +182,11 @@ def edit_file_matlab(filename: str):
         engine = MatlabHelper().get_local_engine()
     except Exception as ex:
         LOGGER.error("Attempted to edit a file in MATLAB engine", exc_info=ex)
-        return
+        return False
 
+    engine.cd(os.getcwd())
     engine.edit(str(filename))
+    return True
 
 
 class Singleton(type(QtWidgets.QDialog), type):
@@ -182,7 +328,7 @@ def open_file(self, file, language):
 
         if self.editor.lexer() is not None:
             self.editor.lexer().setFont(self.default_font)
-        self.unchanged_text = self.file.read_text()
+        self.unchanged_text = self.file.read_text(encoding="utf-8", errors="backslashreplace")
         self.editor.setText(self.unchanged_text)
         self.editor.setModified(False)
         self.setWindowModified(False)
@@ -198,7 +344,7 @@ def save_file(self):
             return
 
         try:
-            self.file.write_text(self.editor.text())
+            self.file.write_text(self.editor.text(), encoding="utf-8")
             self.unchanged_text = self.editor.text()
             self.show_modified()
         except OSError as ex:
diff --git a/rascal2/dialogs/settings_dialog.py b/rascal2/dialogs/settings_dialog.py
index e41d7137..be70e4b1 100644
--- a/rascal2/dialogs/settings_dialog.py
+++ b/rascal2/dialogs/settings_dialog.py
@@ -5,7 +5,7 @@
 
 from PyQt6 import QtCore, QtWidgets
 
-from rascal2.config import LOGGER, MATLAB_ARCH_FILE, MatlabHelper
+from rascal2.config import LOGGER, MATLAB_ARCH_FILE, SETTINGS, MatlabHelper
 from rascal2.settings import SettingsGroups
 from rascal2.widgets.inputs import get_validated_input
 
@@ -26,7 +26,7 @@ def __init__(self, parent):
         self.setMinimumWidth(600)
         self.setMinimumHeight(400)
 
-        self.settings = parent.settings.copy()
+        self.settings = SETTINGS.copy()
         self.matlab_tab = MatlabSetupTab()
         self.reset_dialog = None
 
@@ -60,14 +60,14 @@ def __init__(self, parent):
 
     def update_settings(self) -> None:
         """Accept the changed settings."""
-        self.parent().settings = self.settings
-        self.parent().settings.set_global_settings()
+        vars(SETTINGS).update(vars(self.settings))
+        SETTINGS.set_global_settings()
         self.matlab_tab.set_matlab_paths()
         self.accept()
 
     def reset_default_settings(self) -> None:
         """Reset the settings to the global defaults."""
-        self.parent().settings.reset_global_settings()
+        SETTINGS.reset_global_settings()
         self.accept()
 
 
diff --git a/rascal2/settings.py b/rascal2/settings.py
index db6873fe..37619b2b 100644
--- a/rascal2/settings.py
+++ b/rascal2/settings.py
@@ -56,7 +56,7 @@ class Styles(StrEnum):
 
 
 class BackgroundColour(StrEnum):
-    """Background colour for plot exportRasCAL-2."""
+    """Background colour for plot export."""
 
     Transparent = "none"
     White = "white"
@@ -119,13 +119,17 @@ class Settings(BaseModel, validate_assignment=True, arbitrary_types_allowed=True
     # The global settings are read and written via this object using `set_global_settings`.
     style: Styles = Field(default=Styles.Light, title=SettingsGroups.General, description="Style")
     editor_fontsize: int = Field(default=12, title=SettingsGroups.General, description="Editor Font Size", gt=0)
+    matlab_as_default_editor: bool = Field(
+        default=False,
+        title=SettingsGroups.General,
+        description="Use MATLAB as Default Editor if available.",
+    )
     live_recalculate: bool = Field(
         default=True, title=SettingsGroups.General, description="Auto-run simulation when parameter values change."
     )
     show_stop_calculation_warning: bool = Field(
         default=True, title=SettingsGroups.General, description="Warn when Bayesian calculation is stopped manually."
     )
-
     clear_terminal: bool = Field(
         default=True, title=SettingsGroups.Terminal, description="Clear Terminal when Run Starts"
     )
diff --git a/rascal2/ui/model.py b/rascal2/ui/model.py
index 40423c68..56b581a7 100644
--- a/rascal2/ui/model.py
+++ b/rascal2/ui/model.py
@@ -138,6 +138,14 @@ def save_project(self, save_path):
         self.project.save(Path(save_path, "project.json"))
         if self.results:
             self.results.save(Path(save_path, "results.json"))
+
+        if self.save_path != save_path:
+            for file in self.project.custom_files:
+                if not file.path.is_absolute():
+                    cur_path = Path(self.save_path) / file.path / file.filename
+                    new_dir = Path(save_path) / file.path
+                    shutil.copy(cur_path, new_dir)
+
         self.save_path = save_path
         os.chdir(save_path)
 
@@ -184,6 +192,9 @@ def load_project(self, load_path: str):
         project_file = Path(load_path, "project.json")
         try:
             project = rat.Project.load(project_file)
+            for file in project.custom_files:
+                if file.path.is_relative_to(load_path):
+                    file.path = file.path.relative_to(load_path)
         except JSONDecodeError as err:
             raise ValueError("The project.json file for this project contains invalid JSON.") from err
         except (KeyError, ValueError) as err:
diff --git a/rascal2/ui/presenter.py b/rascal2/ui/presenter.py
index 3dcf7811..5e88b36d 100644
--- a/rascal2/ui/presenter.py
+++ b/rascal2/ui/presenter.py
@@ -1,3 +1,4 @@
+import os
 import re
 import warnings
 from typing import Any
@@ -5,7 +6,7 @@
 import ratapi as rat
 import ratapi.wrappers
 
-from rascal2.config import LOGGER, MatlabHelper
+from rascal2.config import LOGGER, SETTINGS, MatlabHelper
 from rascal2.core import commands
 from rascal2.core.enums import UnsavedReply
 from rascal2.core.runner import LogData, RATRunner
@@ -71,16 +72,19 @@ def load_r1_project(self, load_path: str):
 
     def initialise_ui(self):
         """Initialise UI for a project."""
-        suffix = " [Example]" if self.model.is_project_example() else f"[{self.model.save_path}]"
-        self.view.setWindowTitle(
-            self.view.windowTitle().split(" - ")[0] + " - " + self.model.project.name + suffix,
-        )
+        self.update_title()
         self.view.setup_mdi()
         self.view.plot_widget.update_plots()
         self.view.handle_results(self.model.results)
         self.view.undo_stack.clear()
         self.view.enable_elements()
 
+    def update_title(self):
+        suffix = " [Example]" if self.model.is_project_example() else f"[{self.model.save_path}]"
+        self.view.setWindowTitle(
+            self.view.windowTitle().split(" - ")[0] + " - " + self.model.project.name + suffix,
+        )
+
     def edit_controls(self, setting: str, value: Any):
         """Edit a setting in the Controls object.
 
@@ -116,6 +120,13 @@ def save_project(self, save_as: bool = False):
             Indicates if the project was saved.
         """
         to_path = self.model.save_path
+        if self.view.project_widget.stacked_widget.currentIndex() != 0:
+            # User is still editing the project
+            self.view.show_message(
+                "The project window is still editing, please accept changes or cancel before saving to file."
+            )
+            return False
+
         if save_as or self.model.is_project_example():
             to_path = self.view.get_project_folder()
             if not to_path:
@@ -126,6 +137,7 @@ def save_project(self, save_as: bool = False):
             LOGGER.error(f"Failed to save project to {to_path}.\n", exc_info=err)
         else:
             update_recent_projects(self.model.save_path)
+            self.update_title()
             self.view.undo_stack.setClean()
         return True
 
@@ -190,14 +202,15 @@ def quick_run(self, project=None):
             [file.language == "matlab" for file in self.model.project.custom_files]
         ):
             matlab_helper = MatlabHelper()
-            matlab_helper.get_local_engine()
+            engine = matlab_helper.get_local_engine()
+            engine.cd(os.getcwd())
         return rat.run(project, rat.Controls(display="off"))[1]
 
     def run(self):
         """Run rat using multiprocessing."""
         # reset terminal
         self.view.terminal_widget.progress_bar.setVisible(False)
-        if self.view.settings.clear_terminal:
+        if SETTINGS.clear_terminal:
             self.view.terminal_widget.clear()
 
         # hide bayes plots button so users can't open plots during run
@@ -211,6 +224,7 @@ def run(self):
         self.runner.finished.connect(self.handle_results)
         self.runner.stopped.connect(self.handle_interrupt)
         self.runner.event_received.connect(self.handle_event)
+        self.view.terminal_widget.write("Initializing RAT Process...")
         self.runner.start()
 
     def handle_results(self):
diff --git a/rascal2/ui/view.py b/rascal2/ui/view.py
index ff61efeb..2420abe0 100644
--- a/rascal2/ui/view.py
+++ b/rascal2/ui/view.py
@@ -2,12 +2,12 @@
 
 from PyQt6 import QtCore, QtGui, QtWidgets
 
-from rascal2.config import EXAMPLES_PATH, EXAMPLES_TEMP_PATH, path_for
+from rascal2.config import EXAMPLES_PATH, EXAMPLES_TEMP_PATH, SETTINGS, path_for
 from rascal2.core.enums import UnsavedReply
 from rascal2.dialogs.about_dialog import AboutDialog
 from rascal2.dialogs.settings_dialog import SettingsDialog
 from rascal2.dialogs.startup_dialog import PROJECT_FILES, LoadDialog, LoadR1Dialog, NewProjectDialog, StartupDialog
-from rascal2.settings import MDIGeometries, Settings, get_global_settings
+from rascal2.settings import MDIGeometries, get_global_settings
 from rascal2.widgets import ControlsWidget, PlotWidget, TerminalWidget
 from rascal2.widgets.project import ProjectWidget
 from rascal2.widgets.startup import StartUpWidget
@@ -50,7 +50,6 @@ def __init__(self):
         self.setMinimumSize(1360, 800)
         self.setAttribute(QtCore.Qt.WidgetAttribute.WA_DeleteOnClose)
 
-        self.settings = Settings()
         self.startup_dlg = StartUpWidget(self)
         self.setCentralWidget(self.startup_dlg)
 
@@ -493,7 +492,7 @@ def show_confirm_stop_calculation_dialog(self) -> bool:
         bool
             Whether the confirmation was affirmative.
         """
-        if not self.settings.show_stop_calculation_warning:
+        if not SETTINGS.show_stop_calculation_warning:
             return True
 
         message_box = QtWidgets.QMessageBox(self)
@@ -509,7 +508,7 @@ def show_confirm_stop_calculation_dialog(self) -> bool:
         message_box.setCheckBox(no_show_check_box)
         no_show_check_box.toggled.connect(lambda val: setattr(self.settings, "show_stop_calculation_warning", not val))
         message_box.exec()
-        self.settings.set_global_settings()
+        SETTINGS.set_global_settings()
         return message_box.clickedButton() == yes_button
 
     def show_unsaved_dialog(self, message: str) -> UnsavedReply:
@@ -541,6 +540,16 @@ def show_unsaved_dialog(self, message: str) -> UnsavedReply:
         else:
             return UnsavedReply.Cancel
 
+    def show_message(self, message):
+        """Show message to the user.
+
+        Parameters
+        ----------
+        message : str
+            user message
+        """
+        QtWidgets.QMessageBox.information(self, MAIN_WINDOW_TITLE, message)
+
     def check_save_blacklist(self, save_path):
         """Check if user selected save path is invalid i.e. in the examples or tmp directory.
 
diff --git a/rascal2/widgets/inputs.py b/rascal2/widgets/inputs.py
index 092e887a..6d6d3015 100644
--- a/rascal2/widgets/inputs.py
+++ b/rascal2/widgets/inputs.py
@@ -1,5 +1,6 @@
 """Widgets for validated user inputs."""
 
+import os
 from collections.abc import Callable, Iterable
 from enum import Enum
 from math import floor, log10
@@ -176,7 +177,7 @@ def __init__(self, parent):
 
         self.open_on_show = False
         self.setAutoFillBackground(True)
-        self.path = ""
+        self.path = os.getcwd()
 
     def mouseDoubleClickEvent(self, event):
         self.open()
diff --git a/rascal2/widgets/plot.py b/rascal2/widgets/plot.py
index 241c480a..67bd34a3 100644
--- a/rascal2/widgets/plot.py
+++ b/rascal2/widgets/plot.py
@@ -8,7 +8,7 @@
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg, NavigationToolbar2QT
 from PyQt6 import QtCore, QtGui, QtWidgets
 
-from rascal2.config import path_for
+from rascal2.config import SETTINGS, path_for
 from rascal2.widgets.inputs import MultiSelectComboBox, ProgressButton
 
 
@@ -348,10 +348,9 @@ def export(self):
         """Save the figure to a file."""
         filepath, accepted = QtWidgets.QFileDialog.getSaveFileName(self, "Export Plot", filter="Image File (*.png)")
         if accepted:
-            settings = self.parent.parent.settings
             sx = self.figure.get_figwidth() * self.figure.dpi
             dpi = self.figure.dpi if sx > 1920 else 1920 // self.figure.get_figwidth()
-            self.figure.savefig(filepath, facecolor=settings.export_background_colour, dpi=dpi)
+            self.figure.savefig(filepath, facecolor=SETTINGS.export_background_colour, dpi=dpi)
 
 
 class RefSLDWidget(AbstractPlotWidget):
@@ -434,6 +433,9 @@ def plot(self, project: ratapi.Project, results: ratapi.outputs.Results | ratapi
         results : Union[ratapi.outputs.Results, ratapi.outputs.BayesResults]
             The calculation results.
         """
+        if project is None or results is None:
+            return
+
         data = ratapi.events.PlotEventData()
 
         data.modelType = project.model
diff --git a/rascal2/widgets/project/lists.py b/rascal2/widgets/project/lists.py
index 1be14d8e..991ca4ed 100644
--- a/rascal2/widgets/project/lists.py
+++ b/rascal2/widgets/project/lists.py
@@ -9,7 +9,7 @@
 from PyQt6 import QtCore, QtGui, QtWidgets
 from ratapi.utils.enums import BackgroundActions, LayerModels
 
-from rascal2.config import path_for
+from rascal2.config import SETTINGS, path_for
 from rascal2.core.readers import readers
 from rascal2.widgets.delegates import ProjectFieldDelegate
 from rascal2.widgets.inputs import RangeWidget
@@ -683,11 +683,9 @@ def update_project(self, index, prop, value):
         if not self.edit_mode:
             presenter = self.parent.parent.parent.presenter
             presenter.model.blockSignals(True)
-            presenter.edit_project(
-                {"contrasts": self.model.classlist}, preview=presenter.view.settings.live_recalculate
-            )
+            presenter.edit_project({"contrasts": self.model.classlist}, preview=SETTINGS.live_recalculate)
             presenter.model.blockSignals(False)
-            if presenter.view.settings.live_recalculate:
+            if SETTINGS.live_recalculate:
                 presenter.view.plot_widget.update_plots()
 
     def set_name_data(self, index: int, name: str):
@@ -912,9 +910,9 @@ def update_project_data(self):
         """Update parent project data and recalculate plots."""
         presenter = self.parent.parent.parent.presenter
         presenter.model.blockSignals(True)
-        presenter.edit_project({"data": self.model.classlist}, preview=presenter.view.settings.live_recalculate)
+        presenter.edit_project({"data": self.model.classlist}, preview=SETTINGS.live_recalculate)
         presenter.model.blockSignals(False)
-        if presenter.view.settings.live_recalculate:
+        if SETTINGS.live_recalculate:
             presenter.view.plot_widget.update_plots()
 
     def set_name_data(self, index: int, name: str):
diff --git a/rascal2/widgets/project/project.py b/rascal2/widgets/project/project.py
index 442521ff..d0c846f2 100644
--- a/rascal2/widgets/project/project.py
+++ b/rascal2/widgets/project/project.py
@@ -1,5 +1,7 @@
 """Widget for the Project window."""
 
+import os
+import pathlib
 from collections.abc import Generator
 from copy import deepcopy
 
@@ -433,6 +435,27 @@ def validate_draft_project(self) -> Generator[str, None, None]:
         """Get all errors with the draft project."""
         yield from self.validate_layers()
         yield from self.validate_contrasts()
+        yield from self.validate_custom_file()
+
+    def validate_custom_file(self) -> Generator[str, None, None]:
+        """Ensure that all custom files in the draft project are valid, and yield errors if not.
+
+        Yields
+        ------
+        str
+            The message for each error in custom files.
+
+        """
+        project = self.draft_project
+        for file in project["custom_files"]:
+            if not file.filename:
+                msg = f"Custom file ({file.name}) does not have a valid filename."
+                yield msg
+            if file.filename:
+                path = file.path if file.path else os.getcwd()
+                if not (pathlib.Path(path) / file.filename).exists():
+                    msg = f"Custom file ({file.name}) could not be found in the given path {path}."
+                    yield msg
 
     def validate_layers(self) -> Generator[str, None, None]:
         """Ensure that all layers in the draft project are valid, and yield errors if not.
diff --git a/rascal2/widgets/project/slider_view.py b/rascal2/widgets/project/slider_view.py
index d3e285d4..09a10fcf 100644
--- a/rascal2/widgets/project/slider_view.py
+++ b/rascal2/widgets/project/slider_view.py
@@ -3,6 +3,8 @@
 import ratapi
 from PyQt6 import QtCore, QtGui, QtWidgets
 
+from rascal2.config import LOGGER
+
 
 class SliderViewWidget(QtWidgets.QWidget):
     """The slider view widget which allows user change fitted parameters with sliders."""
@@ -97,8 +99,11 @@ def update_result_and_plots(self):
         """Update and plot result when sliders are changed."""
         project = ratapi.Project()
         vars(project).update(self.draft_project)
-        results = self._parent.presenter.quick_run(project)
-        self._parent.plot_widget.reflectivity_plot.plot(project, results)
+        try:
+            results = self._parent.presenter.quick_run(project)
+            self._parent.plot_widget.reflectivity_plot.plot(project, results)
+        except Exception as ex:
+            LOGGER.error("Attempt to update slider preview failed", exc_info=ex)
 
     def _cancel_changes_from_sliders(self):
         """Revert changes to parameter values and close slider view."""
diff --git a/rascal2/widgets/project/tables.py b/rascal2/widgets/project/tables.py
index 0050c6a1..38179391 100644
--- a/rascal2/widgets/project/tables.py
+++ b/rascal2/widgets/project/tables.py
@@ -1,18 +1,21 @@
 """Models and widgets for project fields."""
 
 import contextlib
+import os
 import re
+import shutil
 from enum import Enum
 from pathlib import Path
 
 import pydantic
 import ratapi
 from PyQt6 import QtCore, QtGui, QtWidgets
-from ratapi.utils.enums import Languages, Procedures, TypeOptions
+from ratapi.utils.enums import Calculations, Languages, Procedures, TypeOptions
 
 import rascal2.widgets.delegates as delegates
-from rascal2.config import path_for
-from rascal2.dialogs.custom_file_editor import edit_file, edit_file_matlab
+from rascal2.config import LOGGER, SETTINGS, path_for
+from rascal2.core.enums import CustomFileType
+from rascal2.dialogs.custom_file_editor import create_new_file, edit_file
 
 
 class ClassListTableModel(QtCore.QAbstractTableModel):
@@ -317,11 +320,9 @@ def update_project(self, recalculate: bool):
         """
         presenter = self.parent.parent.parent.presenter
         presenter.model.blockSignals(True)
-        presenter.edit_project(
-            {self.field: self.model.classlist}, preview=recalculate and presenter.view.settings.live_recalculate
-        )
+        presenter.edit_project({self.field: self.model.classlist}, preview=recalculate and SETTINGS.live_recalculate)
         presenter.model.blockSignals(False)
-        if presenter.view.settings.live_recalculate:
+        if SETTINGS.live_recalculate:
             presenter.view.plot_widget.update_plots()
 
 
@@ -577,6 +578,7 @@ def __init__(self, classlist: ratapi.ClassList, parent: QtWidgets.QWidget):
         self.func_names = {}
         self.headers.remove("path")
         self.col_offset = 2
+        self.always_copy = True
 
     def flags(self, index):
         flags = super().flags(index)
@@ -594,12 +596,18 @@ def data(self, index, role=QtCore.Qt.ItemDataRole.DisplayRole):
             elif role in [QtCore.Qt.ItemDataRole.ToolTipRole, QtCore.Qt.ItemDataRole.UserRole]:
                 display = super().data(index, QtCore.Qt.ItemDataRole.DisplayRole)
                 if display != "" and display != "Browse...":
-                    return self.classlist[index.row()].path.as_posix()
+                    path = Path(self.classlist[index.row()].path)
+                    if not path.is_absolute():
+                        path = Path(os.getcwd()) / self.classlist[index.row()].path
+                    return path.as_posix()
         return data
 
     def setData(self, index, value, role=QtCore.Qt.ItemDataRole.DisplayRole):
         if self.index_header(index) == "filename" and value != "Browse...":
             file_path = Path(value)
+            if self.always_copy:
+                file_path = self.copy_custom_file(file_path)
+
             row = index.row()
             self.classlist[row].path = file_path.parent
             self.classlist[row].filename = str(file_path.name)
@@ -614,7 +622,9 @@ def setData(self, index, value, role=QtCore.Qt.ItemDataRole.DisplayRole):
                     # (?:^|\n) means 'match start of the string (i.e. the file) or a newline'
                     # (\S+) means 'capture one or more non-whitespace characters'
                     # so the regex captures a word between 'def ' and '(', i.e. a function name
-                    func_names = re.findall(r"(?:^|\n)def (\S+)\(", file_path.read_text())
+                    func_names = re.findall(
+                        r"(?:^|\n)def (\S+)\(", file_path.read_text(encoding="utf-8", errors="backslashreplace")
+                    )
                 case ".m":
                     language = Languages.Matlab
                     func_names = None
@@ -635,6 +645,31 @@ def setData(self, index, value, role=QtCore.Qt.ItemDataRole.DisplayRole):
 
         return super().setData(index, value, role)
 
+    @staticmethod
+    def copy_custom_file(file_path):
+        """Copy given custom file to the project directory.
+
+        Parameters
+        ----------
+        file_path : str
+            The custom file to copy.
+        """
+        file_path = Path(file_path)
+        project_dir = os.getcwd()
+        if not file_path.is_relative_to(project_dir):
+            try:
+                file_path = Path(shutil.copy(file_path, project_dir)).relative_to(project_dir)
+            except shutil.SameFileError:
+                # Attempting to copy a file to the same directory it is in
+                # should fail quietly since file is already copied.
+                pass
+            except OSError as ex:
+                LOGGER.error("Attempt to copy custom file failed, full path will be used.", exc_info=ex)
+        else:
+            file_path = file_path.relative_to(project_dir)
+
+        return file_path
+
     def append_item(self):
         """Append an item to the ClassList."""
         self.classlist.append(self.item_type(filename="", path="/"))
@@ -646,65 +681,114 @@ class CustomFileWidget(ProjectFieldWidget):
 
     classlist_model = CustomFileModel
 
+    def __init__(self, field: str, parent):
+        super().__init__(field, parent)
+
+        layout = self.layout().itemAt(0)  # topbar layout
+        self.copy_checkbox = QtWidgets.QCheckBox("Always Copy")
+        self.copy_checkbox.setChecked(True)
+        self.copy_checkbox.setHidden(True)
+        self.copy_checkbox.checkStateChanged.connect(self.update_copy_state)
+        self.copy_checkbox.setToolTip("Indicates if files should be copied when outside project folder.")
+        layout.insertWidget(layout.count() - 1, self.copy_checkbox)
+        self.edit_file_column = 1
+
+    def update_model(self, classlist: ratapi.classlist.ClassList):
+        super().update_model(classlist)
+        self.model.dataChanged.connect(lambda index: self.setup_button(index.row()))
+
+    def update_copy_state(self, state):
+        """Update the always_copy state.
+
+        Parameters
+        ----------
+        state : QtCore.Qt.CheckState
+            Indicates the always_copy state.
+        """
+        self.model.always_copy = state == QtCore.Qt.CheckState.Checked
+
     def edit(self):
         super().edit()
-        edit_file_column = 1
-        self.table.showColumn(edit_file_column)
-        # disconnect from old table's buttons so they don't create dangling references
-        # if no connections currently exist (i.e. table empty), disconnect() raises a TypeError
-        with contextlib.suppress(TypeError):
-            self.model.dataChanged.disconnect()
+        self.copy_checkbox.setHidden(False)
+        self.table.showColumn(self.edit_file_column)
         for i in range(0, self.model.rowCount()):
-            self.table.setIndexWidget(self.model.index(i, edit_file_column), self.make_edit_button(i))
+            self.table.setIndexWidget(
+                self.model.index(i, self.edit_file_column), QtWidgets.QPushButton("Edit File", self.table)
+            )
+            self.setup_button(i)
         self.resize_columns()
 
-    def make_edit_button(self, index):
-        button = QtWidgets.QPushButton("Edit File", self.table)
-        q_scintilla_action = QtGui.QAction("Edit in RasCAL-2...", self.table)
-        q_scintilla_action.triggered.connect(
+    def setup_button(self, row):
+        """Check whether the button should be editable and set it up for the right language.
+
+        Parameters
+        ----------
+        row : int
+            The row containing the button to setup.
+        """
+        language = self.model.data(self.model.index(row, self.model.headers.index("language") + self.model.col_offset))
+        button = self.table.indexWidget(self.model.index(row, self.edit_file_column))
+
+        edit_file_action = QtGui.QAction("Edit File...", self.table)
+        edit_file_action.triggered.connect(
             lambda: edit_file(
-                self.model.classlist[index].path / self.model.classlist[index].filename,
-                self.model.classlist[index].language,
+                self.model.classlist[row].path / self.model.classlist[row].filename,
+                self.model.classlist[row].language,
                 self,
             )
         )
-        matlab_action = QtGui.QAction("Edit in MATLAB...", self.table)
-        matlab_action.triggered.connect(
-            lambda: edit_file_matlab(self.model.classlist[index].path / self.model.classlist[index].filename)
-        )
-        menu = QtWidgets.QMenu(self.table)
-        menu.addActions([q_scintilla_action, matlab_action])
+        new_model_file_action = QtGui.QAction("New Model File...", self.table)
+        new_model_file_action.triggered.connect(lambda: self.create_new_file(row, CustomFileType.Model))
+        new_background_file_action = QtGui.QAction("New Background File...", self.table)
+        new_background_file_action.triggered.connect(lambda: self.create_new_file(row, CustomFileType.Background))
 
-        def setup_button():
-            """Check whether the button should be editable and set it up for the right language."""
-            language = self.model.data(
-                self.model.index(index, self.model.headers.index("language") + self.model.col_offset)
-            )
-            with contextlib.suppress(TypeError):
-                button.pressed.disconnect()
-            if language == Languages.Matlab:
+        with contextlib.suppress(TypeError):
+            button.pressed.disconnect()
+
+        button.setMenu(None)
+        filename_index = self.model.index(row, self.model.headers.index("filename") + self.model.col_offset)
+        if language in [Languages.Matlab, Languages.Python]:
+            if self.model.data(filename_index) == "Browse...":
+                menu = QtWidgets.QMenu(self.table)
+                menu.addActions([new_model_file_action, new_background_file_action])
                 button.setMenu(menu)
                 button.pressed.connect(button.showMenu)
+                button.setText("New File")
             else:
-                button.setMenu(None)
-                button.pressed.connect(
-                    lambda: edit_file(
-                        self.model.classlist[index].path / self.model.classlist[index].filename,
-                        self.model.classlist[index].language,
-                        self,
-                    )
-                )
+                button.pressed.connect(edit_file_action.trigger)
+                button.setText("Edit File")
+            editable = True
+        else:
+            button.setText("")
+            editable = False
+        button.setEnabled(editable)
 
-            editable = (language in [Languages.Matlab, Languages.Python]) and (
-                self.model.data(self.model.index(index, self.model.headers.index("filename") + self.model.col_offset))
-                != "Browse..."
-            )
-            button.setEnabled(editable)
+    def create_new_file(self, row, file_type):
+        """Create a new custom file for given model entry.
 
-        setup_button()
-        self.model.dataChanged.connect(lambda: setup_button())
+        Parameters
+        ----------
+        row : int
+            The row to create file for.
+        file_type : CustomFileType
+            The type of custom file to create.
+        """
+        is_domains = self.parent.parent.calculation_combobox.currentText() == Calculations.Domains
+        try:
+            filename = create_new_file(
+                self.model.classlist[row].name,
+                self.model.classlist[row].language,
+                is_domains,
+                file_type,
+                self,
+            )
+        except OSError as ex:
+            LOGGER.error("Attempt to create new custom file failed.", exc_info=ex)
+            return
 
-        return button
+        if filename:
+            index = self.model.index(row, self.model.headers.index("filename") + self.model.col_offset)
+            self.model.setData(index, filename, QtCore.Qt.ItemDataRole.EditRole)
 
     def set_item_delegates(self):
         super().set_item_delegates()
@@ -759,16 +843,16 @@ class BackgroundsModel(AbstractSignalModel):
     """Model for classlists of Backgrounds."""
 
     @property
-    def num_valid_values(self) -> tuple[int]:
-        return (0, 1, 5)
+    def num_valid_values(self) -> tuple[int, int, int]:
+        return 0, 1, 5
 
 
 class ResolutionsModel(AbstractSignalModel):
     """Model for classlists of Resolutions."""
 
     @property
-    def num_valid_values(self) -> tuple[int]:
-        return (0, -1, 5)  # -1 to remove 'source' field for data resolutions
+    def num_valid_values(self) -> tuple[int, int, int]:
+        return 0, -1, 5  # -1 to remove 'source' field for data resolutions
 
 
 class AbstractSignalFieldWidget(ProjectFieldWidget):
diff --git a/requirements.txt b/requirements.txt
index 07b0acd6..1fc5bca6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 PyInstaller==6.9.0
 PyQt6==6.7.1
 PyQt6-Qt6==6.7.3
-ratapi==0.0.0.dev12
+ratapi==0.0.0.dev13
 pydantic==2.8.2
 PyQt6-QScintilla==2.14.1
 nexusformat==1.0.7
diff --git a/tests/dialogs/test_custom_file_editor.py b/tests/dialogs/test_custom_file_editor.py
index 8c3bc09c..e2189814 100644
--- a/tests/dialogs/test_custom_file_editor.py
+++ b/tests/dialogs/test_custom_file_editor.py
@@ -9,7 +9,7 @@
 from PyQt6 import Qsci, QtWidgets
 from ratapi.utils.enums import Languages
 
-from rascal2.dialogs.custom_file_editor import CustomFileEditorDialog, edit_file, edit_file_matlab
+from rascal2.dialogs.custom_file_editor import CustomFileEditorDialog, edit_file_local, edit_file_matlab
 
 parent = QtWidgets.QMainWindow()
 
@@ -32,12 +32,12 @@ def temp_file():
 
 
 @patch("rascal2.dialogs.custom_file_editor.CustomFileEditorDialog.show")
-def test_edit_file(exec_mock):
-    """Test that the dialog is executed when edit_file() is called on a valid file."""
+def test_edit_file_local(exec_mock):
+    """Test that the dialog is executed when edit_file_local() is called on a valid file."""
     with tempfile.TemporaryDirectory() as tmp:
         file = Path(tmp, "testfile.py")
         file.touch()
-        edit_file(file, Languages.Python, parent)
+        edit_file_local(file, Languages.Python, parent)
 
         exec_mock.assert_called_once()
 
@@ -48,7 +48,7 @@ def test_edit_incorrect_file(dialog_mock, filepath, caplog):
     """A logger error should be emitted if a directory or nonexistent file is given to the editor."""
     with tempfile.TemporaryDirectory() as tmp:
         file = Path(tmp, filepath)
-        edit_file(file, Languages.Python, parent)
+        edit_file_local(file, Languages.Python, parent)
 
     errors = [record for record in caplog.get_records("call") if record.levelno == logging.ERROR]
     assert len(errors) == 1
diff --git a/tests/ui/test_presenter.py b/tests/ui/test_presenter.py
index 156a0373..3f42fe32 100644
--- a/tests/ui/test_presenter.py
+++ b/tests/ui/test_presenter.py
@@ -38,11 +38,14 @@ def __init__(self):
         super().__init__()
         self.undo_stack = MockUndoStack()
         self.controls_widget = MagicMock()
+        self.project_widget = MagicMock()
         self.terminal_widget = MagicMock()
         self.plot_widget = MagicMock()
         self.handle_results = MagicMock()
         self.settings = MagicMock()
         self.get_project_folder = lambda: "new path/"
+        self.windowTitle = lambda: "RasCAL2"
+        self.show_message = MagicMock()
 
 
 @pytest.fixture
@@ -55,6 +58,7 @@ def presenter():
         pr.runner = MagicMock()
         pr.model.controls = Controls()
         pr.model.project = MagicMock()
+        pr.model.project.name = "test_name"
         pr.model.results = MagicMock()
         pr.model.save_path = "some_path/"
         pr.logger = mock_log
@@ -200,7 +204,9 @@ def test_load_project(presenter, function):
 def test_save_project(recent_projects_mock, presenter):
     """Test that projects can be saved, optionally saved as a new folder."""
     presenter.model.project = MagicMock()
+    presenter.model.project.name = "test_name"
     presenter.model.controls = MagicMock()
+    presenter.view.project_widget.stacked_widget.currentIndex = MagicMock(return_value=0)
     presenter.save_project()
     presenter.model.project.save.assert_called_once()
     presenter.model.controls.save.assert_called_once()
@@ -228,6 +234,7 @@ def test_ask_to_save_project(presenter, reply, undo_clean_state, expected):
     """Test whether or not to proceed with an event based on the response to the unsaved changes warning."""
     presenter.model.save_project = MagicMock()
     presenter.view.show_unsaved_dialog = MagicMock(return_value=reply)
+    presenter.view.project_widget.stacked_widget.currentIndex = MagicMock(return_value=0)
 
     presenter.view.undo_stack.clean = undo_clean_state
     assert presenter.ask_to_save_project() is expected
diff --git a/tests/widgets/project/test_models.py b/tests/widgets/project/test_models.py
index b99e865e..9fe7067b 100644
--- a/tests/widgets/project/test_models.py
+++ b/tests/widgets/project/test_models.py
@@ -453,6 +453,7 @@ def test_file_model_set_filename(filename, expected_lang, expected_filenames):
     python_file = "def func1(): pass \ndef func2(): pass \ndef func3(): pass"
 
     model = CustomFileModel(init_list, parent)
+    model.always_copy = False
 
     filename_col = model.headers.index("filename") + model.col_offset
     with tempfile.TemporaryDirectory() as tmp:
@@ -477,6 +478,7 @@ def test_file_widget_edit(filename):
 
         widget = CustomFileWidget("files", parent)
         widget.update_model(init_list)
+        widget.model.always_copy = False
 
         edit_col = 1
         assert widget.table.isColumnHidden(edit_col)
@@ -494,12 +496,12 @@ def test_file_widget_edit(filename):
         button = widget.table.indexWidget(widget.model.index(0, edit_col))
         assert isinstance(button, QtWidgets.QPushButton)
 
-        if filename in ["file.m", "file.py"]:
+        if filename in ["file.m", "file.py", ""]:
             assert button.isEnabled()
         else:
             assert not button.isEnabled()
 
-        if filename == "file.m":
+        if filename == "":
             assert button.menu() is not None
             assert len(button.menu().actions()) == 2
         else:
diff --git a/tests/widgets/test_inputs.py b/tests/widgets/test_inputs.py
index a33f9490..6fa7b78d 100644
--- a/tests/widgets/test_inputs.py
+++ b/tests/widgets/test_inputs.py
@@ -4,7 +4,7 @@
     from enum import StrEnum
 except ImportError:
     from strenum import StrEnum
-
+import os
 from pathlib import Path
 
 import pytest
@@ -29,7 +29,7 @@ class MyEnum(StrEnum):
         (FieldInfo(annotation=int), QtWidgets.QSpinBox, 15),
         (FieldInfo(annotation=MyEnum), QtWidgets.QComboBox, "value 2"),
         (FieldInfo(annotation=str), QtWidgets.QLineEdit, "Test string"),
-        (FieldInfo(annotation=Path), PathWidget, str(Path(".").resolve())),
+        (FieldInfo(annotation=Path), PathWidget, Path(".").resolve().as_posix()),
     ],
 )
 def test_editor_type(field_info, expected_type, example_data):
@@ -79,11 +79,8 @@ def test_multi_select_list_update(selected):
 
 def test_path_widget():
     widget = PathWidget(None)
-    assert widget.path == ""
-    assert widget.text() == ""
-
-    widget.setText("Browse...")
-    assert widget.text() == "Browse..."
+    assert widget.path == os.getcwd()
+    assert widget.text() == Path(widget.path).as_posix()
 
     path = Path(".") / "file.m"
     widget.setText(path)