diff --git a/examples/model_coupling/external-linearmodel-ascii.jl b/examples/model_coupling/external-linearmodel-ascii.jl
deleted file mode 120000
index 75b46a9a..00000000
--- a/examples/model_coupling/external-linearmodel-ascii.jl
+++ /dev/null
@@ -1,14 +0,0 @@
-#TODO this does NOT work; `parameters` are not required to be Ordered Dictionary
-paramfile = open("parameters.dat")
-parameters = Meta.parse.(readlines(paramfile))
-close(paramfile)
-
-f(t) = parameters[1] * t - parameters[2] # a * t - b; linear model
-times = 1:4
-predictions = map(f, times)
-
-predicfile = open("predictions.dat", "w")
-for prediction in predictions
-	write(predicfile, string(prediction, "\n"))
-end
-close(predicfile)
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-ascii.jl b/examples/model_coupling/external-linearmodel-ascii.jl
new file mode 100644
index 00000000..75b46a9a
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-ascii.jl
@@ -0,0 +1,14 @@
+#TODO this does NOT work; `parameters` are not required to be Ordered Dictionary
+paramfile = open("parameters.dat")
+parameters = Meta.parse.(readlines(paramfile))
+close(paramfile)
+
+f(t) = parameters[1] * t - parameters[2] # a * t - b; linear model
+times = 1:4
+predictions = map(f, times)
+
+predicfile = open("predictions.dat", "w")
+for prediction in predictions
+	write(predicfile, string(prediction, "\n"))
+end
+close(predicfile)
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-ascii.mads b/examples/model_coupling/external-linearmodel-ascii.mads
deleted file mode 120000
index 33b8c7ed..00000000
--- a/examples/model_coupling/external-linearmodel-ascii.mads
+++ /dev/null
@@ -1,11 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-ascii.jl"
-ASCIIParameters: parameters.dat
-ASCIIPredictions: predictions.dat
diff --git a/examples/model_coupling/external-linearmodel-ascii.mads b/examples/model_coupling/external-linearmodel-ascii.mads
new file mode 100644
index 00000000..33b8c7ed
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-ascii.mads
@@ -0,0 +1,11 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-ascii.jl"
+ASCIIParameters: parameters.dat
+ASCIIPredictions: predictions.dat
diff --git a/examples/model_coupling/external-linearmodel-jld.jl b/examples/model_coupling/external-linearmodel-jld.jl
deleted file mode 120000
index 101dd562..00000000
--- a/examples/model_coupling/external-linearmodel-jld.jl
+++ /dev/null
@@ -1,10 +0,0 @@
-import JLD
-import OrderedCollections
-
-parameters = JLD.load("parameters.jld") # JLD file created to write current model parameters
-JLD
-f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
-times = 1:4
-predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
-
-JLD.save("predictions.jld", predictions) # JLD file created to write current model predictions
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-jld.jl b/examples/model_coupling/external-linearmodel-jld.jl
new file mode 100644
index 00000000..101dd562
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-jld.jl
@@ -0,0 +1,10 @@
+import JLD
+import OrderedCollections
+
+parameters = JLD.load("parameters.jld") # JLD file created to write current model parameters
+JLD
+f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
+times = 1:4
+predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
+
+JLD.save("predictions.jld", predictions) # JLD file created to write current model predictions
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-jld.mads b/examples/model_coupling/external-linearmodel-jld.mads
deleted file mode 120000
index f136c215..00000000
--- a/examples/model_coupling/external-linearmodel-jld.mads
+++ /dev/null
@@ -1,13 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-jld.jl"
-JLDParameters: parameters.jld
-JLDPredictions:
-- predictions.jld
diff --git a/examples/model_coupling/external-linearmodel-jld.mads b/examples/model_coupling/external-linearmodel-jld.mads
new file mode 100644
index 00000000..f136c215
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-jld.mads
@@ -0,0 +1,13 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-jld.jl"
+JLDParameters: parameters.jld
+JLDPredictions:
+- predictions.jld
diff --git a/examples/model_coupling/external-linearmodel-jld2.jl b/examples/model_coupling/external-linearmodel-jld2.jl
deleted file mode 120000
index 4f5a50a6..00000000
--- a/examples/model_coupling/external-linearmodel-jld2.jl
+++ /dev/null
@@ -1,10 +0,0 @@
-import JLD2
-import OrderedCollections
-
-parameters = JLD2.load("parameters.jld2") # JLD file created to write current model parameters
-
-f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
-times = 1:4
-predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
-
-JLD2.save("predictions.jld2", predictions) # JLD file created to write current model predictions
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-jld2.jl b/examples/model_coupling/external-linearmodel-jld2.jl
new file mode 100644
index 00000000..4f5a50a6
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-jld2.jl
@@ -0,0 +1,10 @@
+import JLD2
+import OrderedCollections
+
+parameters = JLD2.load("parameters.jld2") # JLD file created to write current model parameters
+
+f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
+times = 1:4
+predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
+
+JLD2.save("predictions.jld2", predictions) # JLD file created to write current model predictions
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-jld2.mads b/examples/model_coupling/external-linearmodel-jld2.mads
deleted file mode 120000
index 3cfbefba..00000000
--- a/examples/model_coupling/external-linearmodel-jld2.mads
+++ /dev/null
@@ -1,13 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-jld2.jl"
-JLDParameters: parameters.jld2
-JLDPredictions:
-- predictions.jld2
diff --git a/examples/model_coupling/external-linearmodel-jld2.mads b/examples/model_coupling/external-linearmodel-jld2.mads
new file mode 100644
index 00000000..3cfbefba
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-jld2.mads
@@ -0,0 +1,13 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-jld2.jl"
+JLDParameters: parameters.jld2
+JLDPredictions:
+- predictions.jld2
diff --git a/examples/model_coupling/external-linearmodel-json-exp.mads b/examples/model_coupling/external-linearmodel-json-exp.mads
deleted file mode 120000
index d520fd0c..00000000
--- a/examples/model_coupling/external-linearmodel-json-exp.mads
+++ /dev/null
@@ -1,12 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", exp: a*-1 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-json.jl"
-JSONParameters: parameters.json
-JSONPredictions:
-- predictions.json
diff --git a/examples/model_coupling/external-linearmodel-json-exp.mads b/examples/model_coupling/external-linearmodel-json-exp.mads
new file mode 100644
index 00000000..d520fd0c
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-json-exp.mads
@@ -0,0 +1,12 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", exp: a*-1 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-json.jl"
+JSONParameters: parameters.json
+JSONPredictions:
+- predictions.json
diff --git a/examples/model_coupling/external-linearmodel-json.jl b/examples/model_coupling/external-linearmodel-json.jl
deleted file mode 120000
index e621c50f..00000000
--- a/examples/model_coupling/external-linearmodel-json.jl
+++ /dev/null
@@ -1,15 +0,0 @@
-import JSON
-import OrderedCollections
-
-parameters = JSON.parsefile("parameters.json")
-@show parameters
-
-f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
-times = 1:4
-@show map(i -> string("o", i), times), map(f, times)
-predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
-
-@show predictions
-jo = open("predictions.json", "w")
-JSON.print(jo, predictions)
-close(jo)
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-json.jl b/examples/model_coupling/external-linearmodel-json.jl
new file mode 100644
index 00000000..e621c50f
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-json.jl
@@ -0,0 +1,15 @@
+import JSON
+import OrderedCollections
+
+parameters = JSON.parsefile("parameters.json")
+@show parameters
+
+f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
+times = 1:4
+@show map(i -> string("o", i), times), map(f, times)
+predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
+
+@show predictions
+jo = open("predictions.json", "w")
+JSON.print(jo, predictions)
+close(jo)
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-json.mads b/examples/model_coupling/external-linearmodel-json.mads
deleted file mode 120000
index 4aa2a16f..00000000
--- a/examples/model_coupling/external-linearmodel-json.mads
+++ /dev/null
@@ -1,12 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-json.jl"
-JSONParameters: parameters.json
-JSONPredictions:
-- predictions.json
diff --git a/examples/model_coupling/external-linearmodel-json.mads b/examples/model_coupling/external-linearmodel-json.mads
new file mode 100644
index 00000000..4aa2a16f
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-json.mads
@@ -0,0 +1,12 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-json.jl"
+JSONParameters: parameters.json
+JSONPredictions:
+- predictions.json
diff --git a/examples/model_coupling/external-linearmodel-parameters.inst b/examples/model_coupling/external-linearmodel-parameters.inst
deleted file mode 120000
index 4a92c7a6..00000000
--- a/examples/model_coupling/external-linearmodel-parameters.inst
+++ /dev/null
@@ -1 +0,0 @@
-internal-linearmodel-parameters.inst
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-parameters.inst b/examples/model_coupling/external-linearmodel-parameters.inst
new file mode 100644
index 00000000..4a92c7a6
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-parameters.inst
@@ -0,0 +1 @@
+internal-linearmodel-parameters.inst
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-parameters.tpl b/examples/model_coupling/external-linearmodel-parameters.tpl
deleted file mode 120000
index 4704ee1d..00000000
--- a/examples/model_coupling/external-linearmodel-parameters.tpl
+++ /dev/null
@@ -1 +0,0 @@
-internal-linearmodel-parameters.tpl
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-parameters.tpl b/examples/model_coupling/external-linearmodel-parameters.tpl
new file mode 100644
index 00000000..4704ee1d
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-parameters.tpl
@@ -0,0 +1 @@
+internal-linearmodel-parameters.tpl
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-yaml.jl b/examples/model_coupling/external-linearmodel-yaml.jl
deleted file mode 120000
index d771a085..00000000
--- a/examples/model_coupling/external-linearmodel-yaml.jl
+++ /dev/null
@@ -1,14 +0,0 @@
-import OrderedCollections
-import YAML
-
-parameters = YAML.load("parameters.yaml")
-if isfile(parameters)
-	parameters = YAML.load_file(parameters)
-end
-
-f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
-times = 1:4
-predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
-
-@show predictions
-YAML.write_file("predictions.yaml", predictions)
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-yaml.jl b/examples/model_coupling/external-linearmodel-yaml.jl
new file mode 100644
index 00000000..d771a085
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-yaml.jl
@@ -0,0 +1,14 @@
+import OrderedCollections
+import YAML
+
+parameters = YAML.load("parameters.yaml")
+if isfile(parameters)
+	parameters = YAML.load_file(parameters)
+end
+
+f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
+times = 1:4
+predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
+
+@show predictions
+YAML.write_file("predictions.yaml", predictions)
\ No newline at end of file
diff --git a/examples/model_coupling/external-linearmodel-yaml.mads b/examples/model_coupling/external-linearmodel-yaml.mads
deleted file mode 120000
index d43eb2c2..00000000
--- a/examples/model_coupling/external-linearmodel-yaml.mads
+++ /dev/null
@@ -1,13 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-yaml.jl"
-YAMLParameters: parameters.yaml
-YAMLPredictions:
-- predictions.yaml
diff --git a/examples/model_coupling/external-linearmodel-yaml.mads b/examples/model_coupling/external-linearmodel-yaml.mads
new file mode 100644
index 00000000..d43eb2c2
--- /dev/null
+++ b/examples/model_coupling/external-linearmodel-yaml.mads
@@ -0,0 +1,13 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-yaml.jl"
+YAMLParameters: parameters.yaml
+YAMLPredictions:
+- predictions.yaml
diff --git a/examples/model_coupling/internal-linearmodel.jl b/examples/model_coupling/internal-linearmodel.jl
deleted file mode 120000
index 901bf177..00000000
--- a/examples/model_coupling/internal-linearmodel.jl
+++ /dev/null
@@ -1 +0,0 @@
-../models/internal-linear-model/internal-linearmodel.jl
\ No newline at end of file
diff --git a/examples/model_coupling/internal-linearmodel.jl b/examples/model_coupling/internal-linearmodel.jl
new file mode 100644
index 00000000..901bf177
--- /dev/null
+++ b/examples/model_coupling/internal-linearmodel.jl
@@ -0,0 +1 @@
+../models/internal-linear-model/internal-linearmodel.jl
\ No newline at end of file
diff --git a/examples/model_coupling/internal-linearmodel.mads b/examples/model_coupling/internal-linearmodel.mads
deleted file mode 120000
index 71417293..00000000
--- a/examples/model_coupling/internal-linearmodel.mads
+++ /dev/null
@@ -1 +0,0 @@
-../models/internal-linear-model/internal-linearmodel.mads
\ No newline at end of file
diff --git a/examples/model_coupling/internal-linearmodel.mads b/examples/model_coupling/internal-linearmodel.mads
new file mode 100644
index 00000000..71417293
--- /dev/null
+++ b/examples/model_coupling/internal-linearmodel.mads
@@ -0,0 +1 @@
+../models/internal-linear-model/internal-linearmodel.mads
\ No newline at end of file
diff --git a/examples/montecarlo/internal-linearmodel.jl b/examples/montecarlo/internal-linearmodel.jl
deleted file mode 120000
index 901bf177..00000000
--- a/examples/montecarlo/internal-linearmodel.jl
+++ /dev/null
@@ -1 +0,0 @@
-../models/internal-linear-model/internal-linearmodel.jl
\ No newline at end of file
diff --git a/examples/montecarlo/internal-linearmodel.jl b/examples/montecarlo/internal-linearmodel.jl
new file mode 100644
index 00000000..901bf177
--- /dev/null
+++ b/examples/montecarlo/internal-linearmodel.jl
@@ -0,0 +1 @@
+../models/internal-linear-model/internal-linearmodel.jl
\ No newline at end of file
diff --git a/examples/montecarlo/internal-linearmodel.mads b/examples/montecarlo/internal-linearmodel.mads
deleted file mode 120000
index 71417293..00000000
--- a/examples/montecarlo/internal-linearmodel.mads
+++ /dev/null
@@ -1 +0,0 @@
-../models/internal-linear-model/internal-linearmodel.mads
\ No newline at end of file
diff --git a/examples/montecarlo/internal-linearmodel.mads b/examples/montecarlo/internal-linearmodel.mads
new file mode 100644
index 00000000..71417293
--- /dev/null
+++ b/examples/montecarlo/internal-linearmodel.mads
@@ -0,0 +1 @@
+../models/internal-linear-model/internal-linearmodel.mads
\ No newline at end of file
diff --git a/examples/optimization/external-ascii-linearmodel.jl b/examples/optimization/external-ascii-linearmodel.jl
deleted file mode 120000
index 75b46a9a..00000000
--- a/examples/optimization/external-ascii-linearmodel.jl
+++ /dev/null
@@ -1,14 +0,0 @@
-#TODO this does NOT work; `parameters` are not required to be Ordered Dictionary
-paramfile = open("parameters.dat")
-parameters = Meta.parse.(readlines(paramfile))
-close(paramfile)
-
-f(t) = parameters[1] * t - parameters[2] # a * t - b; linear model
-times = 1:4
-predictions = map(f, times)
-
-predicfile = open("predictions.dat", "w")
-for prediction in predictions
-	write(predicfile, string(prediction, "\n"))
-end
-close(predicfile)
\ No newline at end of file
diff --git a/examples/optimization/external-ascii-linearmodel.jl b/examples/optimization/external-ascii-linearmodel.jl
new file mode 100644
index 00000000..75b46a9a
--- /dev/null
+++ b/examples/optimization/external-ascii-linearmodel.jl
@@ -0,0 +1,14 @@
+#TODO this does NOT work; `parameters` are not required to be Ordered Dictionary
+paramfile = open("parameters.dat")
+parameters = Meta.parse.(readlines(paramfile))
+close(paramfile)
+
+f(t) = parameters[1] * t - parameters[2] # a * t - b; linear model
+times = 1:4
+predictions = map(f, times)
+
+predicfile = open("predictions.dat", "w")
+for prediction in predictions
+	write(predicfile, string(prediction, "\n"))
+end
+close(predicfile)
\ No newline at end of file
diff --git a/examples/optimization/external-ascii.mads b/examples/optimization/external-ascii.mads
deleted file mode 120000
index 33b8c7ed..00000000
--- a/examples/optimization/external-ascii.mads
+++ /dev/null
@@ -1,11 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-ascii.jl"
-ASCIIParameters: parameters.dat
-ASCIIPredictions: predictions.dat
diff --git a/examples/optimization/external-ascii.mads b/examples/optimization/external-ascii.mads
new file mode 100644
index 00000000..33b8c7ed
--- /dev/null
+++ b/examples/optimization/external-ascii.mads
@@ -0,0 +1,11 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-ascii.jl"
+ASCIIParameters: parameters.dat
+ASCIIPredictions: predictions.dat
diff --git a/examples/optimization/external-jld-linearmodel.jl b/examples/optimization/external-jld-linearmodel.jl
deleted file mode 120000
index 32bb131c..00000000
--- a/examples/optimization/external-jld-linearmodel.jl
+++ /dev/null
@@ -1,11 +0,0 @@
-import JLD
-
-import OrderedCollections
-
-parameters = JLD2.load("parameters.jld") # JLD file created to write current model parameters
-
-f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
-times = 1:4
-predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
-
-JLD2.save("predictions.jld", predictions) # JLD file created to write current model predictions
\ No newline at end of file
diff --git a/examples/optimization/external-jld-linearmodel.jl b/examples/optimization/external-jld-linearmodel.jl
new file mode 100644
index 00000000..32bb131c
--- /dev/null
+++ b/examples/optimization/external-jld-linearmodel.jl
@@ -0,0 +1,11 @@
+import JLD
+
+import OrderedCollections
+
+parameters = JLD2.load("parameters.jld") # JLD file created to write current model parameters
+
+f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
+times = 1:4
+predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
+
+JLD2.save("predictions.jld", predictions) # JLD file created to write current model predictions
\ No newline at end of file
diff --git a/examples/optimization/external-jld.mads b/examples/optimization/external-jld.mads
deleted file mode 120000
index f136c215..00000000
--- a/examples/optimization/external-jld.mads
+++ /dev/null
@@ -1,13 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-jld.jl"
-JLDParameters: parameters.jld
-JLDPredictions:
-- predictions.jld
diff --git a/examples/optimization/external-jld.mads b/examples/optimization/external-jld.mads
new file mode 100644
index 00000000..f136c215
--- /dev/null
+++ b/examples/optimization/external-jld.mads
@@ -0,0 +1,13 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-jld.jl"
+JLDParameters: parameters.jld
+JLDPredictions:
+- predictions.jld
diff --git a/examples/optimization/external-yaml-linearmodel.jl b/examples/optimization/external-yaml-linearmodel.jl
deleted file mode 120000
index d771a085..00000000
--- a/examples/optimization/external-yaml-linearmodel.jl
+++ /dev/null
@@ -1,14 +0,0 @@
-import OrderedCollections
-import YAML
-
-parameters = YAML.load("parameters.yaml")
-if isfile(parameters)
-	parameters = YAML.load_file(parameters)
-end
-
-f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
-times = 1:4
-predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
-
-@show predictions
-YAML.write_file("predictions.yaml", predictions)
\ No newline at end of file
diff --git a/examples/optimization/external-yaml-linearmodel.jl b/examples/optimization/external-yaml-linearmodel.jl
new file mode 100644
index 00000000..d771a085
--- /dev/null
+++ b/examples/optimization/external-yaml-linearmodel.jl
@@ -0,0 +1,14 @@
+import OrderedCollections
+import YAML
+
+parameters = YAML.load("parameters.yaml")
+if isfile(parameters)
+	parameters = YAML.load_file(parameters)
+end
+
+f(t) = parameters["a"] * t - parameters["b"] # a * t - b; linear model
+times = 1:4
+predictions = OrderedCollections.OrderedDict(zip(map(i -> string("o", i), times), map(f, times)))
+
+@show predictions
+YAML.write_file("predictions.yaml", predictions)
\ No newline at end of file
diff --git a/examples/optimization/external-yaml.mads b/examples/optimization/external-yaml.mads
deleted file mode 120000
index d43eb2c2..00000000
--- a/examples/optimization/external-yaml.mads
+++ /dev/null
@@ -1,13 +0,0 @@
-Parameters:
-- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
-- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
-Observations:
-- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
-- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
-- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
-- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
-Command: "julia external-linearmodel-yaml.jl"
-YAMLParameters: parameters.yaml
-YAMLPredictions:
-- predictions.yaml
diff --git a/examples/optimization/external-yaml.mads b/examples/optimization/external-yaml.mads
new file mode 100644
index 00000000..d43eb2c2
--- /dev/null
+++ b/examples/optimization/external-yaml.mads
@@ -0,0 +1,13 @@
+Parameters:
+- a : { longname: "parameter a", init:  1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- b : { longname: "parameter b", init: -1, type: opt, log: no, step: 0.1, min: -10, max: 10 }
+- c : { longname: "parameter b", init: -1, type: null, log: no, step: 0.1, min: -10, max: 10 }
+Observations:
+- o1: { longname: "observation 1", log: false, max: 20, min: -20, target: -3, weight: 1}
+- o2: { longname: "observation 2", log: false, max: 20, min: -20, target:  1, weight: 1}
+- o3: { longname: "observation 3", log: false, max: 20, min: -20, target:  5, weight: 1}
+- o4: { longname: "observation 4", log: false, max: 20, min: -20, target:  9, weight: 1}
+Command: "julia external-linearmodel-yaml.jl"
+YAMLParameters: parameters.yaml
+YAMLPredictions:
+- predictions.yaml
diff --git a/examples/optimization/internal-linearmodel+template.jl b/examples/optimization/internal-linearmodel+template.jl
deleted file mode 120000
index a51f338f..00000000
--- a/examples/optimization/internal-linearmodel+template.jl
+++ /dev/null
@@ -1 +0,0 @@
-../model_coupling/internal-linearmodel+template.jl
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel+template.jl b/examples/optimization/internal-linearmodel+template.jl
new file mode 100644
index 00000000..a51f338f
--- /dev/null
+++ b/examples/optimization/internal-linearmodel+template.jl
@@ -0,0 +1 @@
+../model_coupling/internal-linearmodel+template.jl
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel+template.mads b/examples/optimization/internal-linearmodel+template.mads
deleted file mode 120000
index 01a32d95..00000000
--- a/examples/optimization/internal-linearmodel+template.mads
+++ /dev/null
@@ -1 +0,0 @@
-../model_coupling/internal-linearmodel+template.mads
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel+template.mads b/examples/optimization/internal-linearmodel+template.mads
new file mode 100644
index 00000000..01a32d95
--- /dev/null
+++ b/examples/optimization/internal-linearmodel+template.mads
@@ -0,0 +1 @@
+../model_coupling/internal-linearmodel+template.mads
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel-parameters.tpl b/examples/optimization/internal-linearmodel-parameters.tpl
deleted file mode 120000
index 47678d3c..00000000
--- a/examples/optimization/internal-linearmodel-parameters.tpl
+++ /dev/null
@@ -1 +0,0 @@
-../model_coupling/internal-linearmodel-parameters.tpl
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel-parameters.tpl b/examples/optimization/internal-linearmodel-parameters.tpl
new file mode 100644
index 00000000..47678d3c
--- /dev/null
+++ b/examples/optimization/internal-linearmodel-parameters.tpl
@@ -0,0 +1 @@
+../model_coupling/internal-linearmodel-parameters.tpl
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel.jl b/examples/optimization/internal-linearmodel.jl
deleted file mode 120000
index 901bf177..00000000
--- a/examples/optimization/internal-linearmodel.jl
+++ /dev/null
@@ -1 +0,0 @@
-../models/internal-linear-model/internal-linearmodel.jl
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel.jl b/examples/optimization/internal-linearmodel.jl
new file mode 100644
index 00000000..901bf177
--- /dev/null
+++ b/examples/optimization/internal-linearmodel.jl
@@ -0,0 +1 @@
+../models/internal-linear-model/internal-linearmodel.jl
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel.mads b/examples/optimization/internal-linearmodel.mads
deleted file mode 120000
index 71417293..00000000
--- a/examples/optimization/internal-linearmodel.mads
+++ /dev/null
@@ -1 +0,0 @@
-../models/internal-linear-model/internal-linearmodel.mads
\ No newline at end of file
diff --git a/examples/optimization/internal-linearmodel.mads b/examples/optimization/internal-linearmodel.mads
new file mode 100644
index 00000000..71417293
--- /dev/null
+++ b/examples/optimization/internal-linearmodel.mads
@@ -0,0 +1 @@
+../models/internal-linear-model/internal-linearmodel.mads
\ No newline at end of file
diff --git a/examples/svr/svr.jl b/examples/svr/svr.jl
deleted file mode 120000
index 32332837..00000000
--- a/examples/svr/svr.jl
+++ /dev/null
@@ -1,44 +0,0 @@
-import Mads
-
-@info("Support Vector Regression (SVR) analysis")
-
-Random.seed!(2017)
-
-md = Mads.loadmadsfile(joinpath("..", "models", "internal-polynomial-model", "internal-polynomial.mads"))
-rootname = Mads.getmadsrootname(md)
-svrexec, svrread, svrsave, svrclean = Mads.makesvrmodel(md, 100)
-
-numberofsamples = 100
-paramdict = Mads.getparamrandom(md, numberofsamples)
-paramarray = hcat(map(i->collect(paramdict[i]), keys(paramdict))...)
-predictions = Mads.forward(md, paramdict)'
-
-Mads.madsinfo("Model predictions ...")
-Mads.spaghettiplot(md, predictions, keyword="w13a-model", format="PNG")
-Mads.display("$rootname-w13a-model-$numberofsamples-spaghetti.png")
-
-@time svrpredictions = svrexec(paramarray)
-@info("SVR discrepancy $(maximum(abs.(svrpredictions .- predictions)))")
-
-Mads.madsinfo("SVR predictions ...")
-Mads.spaghettiplot(md, svrpredictions, keyword="w13a-svr", format="PNG")
-Mads.display("$rootname-w13a-svr-$numberofsamples-spaghetti.png")
-
-sa = Mads.efast(md)
-Mads.plotobsSAresults(md, sa, format="PNG")
-Mads.display("$rootname-efast-385.png")
-
-mdsvr = deepcopy(md)
-mdsvr["Julia model"] = svrexec
-mdsvr["Filename"] = "$rootname-svr.mads"
-
-sasvr = Mads.efast(mdsvr)
-Mads.plotobsSAresults(mdsvr, sasvr, format="PNG")
-Mads.display("$rootname-svr-efast-385.png")
-
-svrsave()
-svrclean()
-svrread()
-svrclean()
-
-Mads.rmdir("svrmodels")
\ No newline at end of file
diff --git a/examples/svr/svr.jl b/examples/svr/svr.jl
new file mode 100644
index 00000000..32332837
--- /dev/null
+++ b/examples/svr/svr.jl
@@ -0,0 +1,44 @@
+import Mads
+
+@info("Support Vector Regression (SVR) analysis")
+
+Random.seed!(2017)
+
+md = Mads.loadmadsfile(joinpath("..", "models", "internal-polynomial-model", "internal-polynomial.mads"))
+rootname = Mads.getmadsrootname(md)
+svrexec, svrread, svrsave, svrclean = Mads.makesvrmodel(md, 100)
+
+numberofsamples = 100
+paramdict = Mads.getparamrandom(md, numberofsamples)
+paramarray = hcat(map(i->collect(paramdict[i]), keys(paramdict))...)
+predictions = Mads.forward(md, paramdict)'
+
+Mads.madsinfo("Model predictions ...")
+Mads.spaghettiplot(md, predictions, keyword="w13a-model", format="PNG")
+Mads.display("$rootname-w13a-model-$numberofsamples-spaghetti.png")
+
+@time svrpredictions = svrexec(paramarray)
+@info("SVR discrepancy $(maximum(abs.(svrpredictions .- predictions)))")
+
+Mads.madsinfo("SVR predictions ...")
+Mads.spaghettiplot(md, svrpredictions, keyword="w13a-svr", format="PNG")
+Mads.display("$rootname-w13a-svr-$numberofsamples-spaghetti.png")
+
+sa = Mads.efast(md)
+Mads.plotobsSAresults(md, sa, format="PNG")
+Mads.display("$rootname-efast-385.png")
+
+mdsvr = deepcopy(md)
+mdsvr["Julia model"] = svrexec
+mdsvr["Filename"] = "$rootname-svr.mads"
+
+sasvr = Mads.efast(mdsvr)
+Mads.plotobsSAresults(mdsvr, sasvr, format="PNG")
+Mads.display("$rootname-svr-efast-385.png")
+
+svrsave()
+svrclean()
+svrread()
+svrclean()
+
+Mads.rmdir("svrmodels")
\ No newline at end of file
diff --git a/src/madsjl.jl b/src/madsjl.jl
old mode 100755
new mode 100644