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+//: Phase 3: Start running a loaded and transformed recipe.
+//:
+//: So far we've seen recipes as lists of instructions, and instructions point
+//: at other recipes. To kick things off mu needs to know how to run certain
+//: 'primitive' recipes. That will then give the ability to run recipes
+//: containing these primitives.
+//:
+//: This layer defines a skeleton with just two primitive recipes: IDLE which
+//: does nothing, and COPY, which can copy numbers from one memory location to
+//: another. Later layers will add more primitives.
+
+:(scenario copy_literal)
+recipe main [
+  1:number <- copy 23
+]
++run: 1:number <- copy 23
++mem: storing 23 in location 1
+
+:(scenario copy)
+recipe main [
+  1:number <- copy 23
+  2:number <- copy 1:number
+]
++run: 2:number <- copy 1:number
++mem: location 1 is 23
++mem: storing 23 in location 2
+
+:(scenario copy_multiple)
+recipe main [
+  1:number, 2:number <- copy 23, 24
+]
++mem: storing 23 in location 1
++mem: storing 24 in location 2
+
+:(before "End Types")
+// Book-keeping while running a recipe.
+//: Later layers will change this.
+struct routine {
+  recipe_ordinal running_recipe;
+  long long int running_step_index;
+  routine(recipe_ordinal r) :running_recipe(r), running_step_index(0) {}
+  bool completed() const;
+};
+
+:(before "End Globals")
+routine* Current_routine = NULL;
+map<string, long long int> Instructions_running;
+map<string, long long int> Locations_read;
+map<string, long long int> Locations_read_by_instruction;
+
+:(code)
+void run(recipe_ordinal r) {
+  routine rr(r);
+  Current_routine = &rr;
+  run_current_routine();
+}
+
+void run_current_routine()
+{  // curly on a separate line, because later layers will modify header
+  while (!Current_routine->completed())  // later layers will modify condition
+  {
+    // Running One Instruction
+//?     Instructions_running[current_recipe_name()]++;
+    if (current_instruction().is_label) { ++current_step_index(); continue; }
+    trace(Initial_callstack_depth+Callstack_depth, "run") << current_instruction().to_string() << end();
+    if (Memory[0] != 0) {
+      raise << "something wrote to location 0; this should never happen\n" << end();
+      Memory[0] = 0;
+    }
+    // Read all ingredients from memory.
+    // Each ingredient loads a vector of values rather than a single value; mu
+    // permits operating on reagents spanning multiple locations.
+    vector<vector<double> > ingredients;
+    if (should_copy_ingredients()) {
+      for (long long int i = 0; i < SIZE(current_instruction().ingredients); ++i) {
+        ingredients.push_back(read_memory(current_instruction().ingredients.at(i)));
+//?         Locations_read[current_recipe_name()] += SIZE(ingredients.back());
+//?         Locations_read_by_instruction[current_instruction().name] += SIZE(ingredients.back());
+      }
+    }
+    // Instructions below will write to 'products'.
+    vector<vector<double> > products;
+    switch (current_instruction().operation) {
+      // Primitive Recipe Implementations
+      case COPY: {
+        copy(ingredients.begin(), ingredients.end(), inserter(products, products.begin()));
+        break;
+      }
+      // End Primitive Recipe Implementations
+      default: {
+        cout << "not a primitive op: " << current_instruction().operation << '\n';
+      }
+    }
+    finish_instruction:
+    if (SIZE(products) < SIZE(current_instruction().products)) {
+      raise << SIZE(products) << " vs " << SIZE(current_instruction().products) << ": failed to write to all products! " << current_instruction().to_string() << end();
+    }
+    else {
+      for (long long int i = 0; i < SIZE(current_instruction().products); ++i) {
+        write_memory(current_instruction().products.at(i), products.at(i));
+      }
+    }
+    // End of Instruction
+    ++current_step_index();
+  }
+  stop_running_current_routine:;
+}
+
+bool should_copy_ingredients() {
+  // End should_copy_ingredients Special-cases
+  return true;
+}
+
+//: Some helpers.
+//: We'll need to override these later as we change the definition of routine.
+//: Important that they return referrences into the routine.
+
+inline long long int& current_step_index() {
+  return Current_routine->running_step_index;
+}
+
+inline const string& current_recipe_name() {
+  return Recipe[Current_routine->running_recipe].name;
+}
+
+inline const instruction& current_instruction() {
+  return Recipe[Current_routine->running_recipe].steps.at(Current_routine->running_step_index);
+}
+
+inline bool routine::completed() const {
+  return running_step_index >= SIZE(Recipe[running_recipe].steps);
+}
+
+//:: Startup flow
+
+//: Step 1: load all .mu files with numeric prefixes (in order)
+:(before "End Load Recipes")
+load_permanently("core.mu");
+transform_all();
+
+//: Step 2: load any .mu files provided at the commandline
+:(before "End Commandline Parsing")
+if (argc > 1) {
+  // skip argv[0]
+  argv++;
+  argc--;
+  // ignore argv past '--'; that's commandline args for 'main'
+  while (argc > 0) {
+    if (string(*argv) == "--") break;
+    load_permanently(*argv);
+    argv++;
+    argc--;
+  }
+  transform_all();
+  if (Run_tests) Recipe.erase(Recipe_ordinal[string("main")]);
+}
+
+//: Step 3: if we aren't running tests, locate a recipe called 'main' and
+//: start running it.
+:(before "End Main")
+if (!Run_tests) {
+  setup();
+//?   Trace_file = "interactive";
+//?   START_TRACING_UNTIL_END_OF_SCOPE;
+//?   Trace_stream->collect_layers.insert("app");
+  run_main(argc, argv);
+  teardown();
+}
+
+:(code)
+void run_main(int argc, char* argv[]) {
+  recipe_ordinal r = Recipe_ordinal[string("main")];
+  if (r) run(r);
+}
+
+:(code)
+void dump_profile() {
+  for (map<string, long long int>::iterator p = Instructions_running.begin(); p != Instructions_running.end(); ++p) {
+    cerr << p->first << ": " << p->second << '\n';
+  }
+  cerr << "== locations read\n";
+  for (map<string, long long int>::iterator p = Locations_read.begin(); p != Locations_read.end(); ++p) {
+    cerr << p->first << ": " << p->second << '\n';
+  }
+  cerr << "== locations read by instruction\n";
+  for (map<string, long long int>::iterator p = Locations_read_by_instruction.begin(); p != Locations_read_by_instruction.end(); ++p) {
+    cerr << p->first << ": " << p->second << '\n';
+  }
+}
+:(before "End One-time Setup")
+//? atexit(dump_profile);
+
+:(code)
+void cleanup_main() {
+  if (!Trace_file.empty() && Trace_stream) {
+    ofstream fout((Trace_dir+Trace_file).c_str());
+    fout << Trace_stream->readable_contents("");
+    fout.close();
+  }
+}
+:(before "End One-time Setup")
+atexit(cleanup_main);
+
+:(code)
+void load_permanently(string filename) {
+  if (is_directory(filename)) {
+    load_all_permanently(filename);
+    return;
+  }
+  ifstream fin(filename.c_str());
+  fin.peek();
+  if (!fin) {
+    raise << "no such file " << filename << '\n' << end();
+    return;
+  }
+  fin >> std::noskipws;
+  load(fin);
+  fin.close();
+  // freeze everything so it doesn't get cleared by tests
+  recently_added_recipes.clear();
+  // End load_permanently.
+}
+
+bool is_directory(string path) {
+  struct stat info;
+  if (stat(path.c_str(), &info)) return false;  // error
+  return info.st_mode & S_IFDIR;
+}
+
+void load_all_permanently(string dir) {
+  dirent** files;
+  int num_files = scandir(dir.c_str(), &files, NULL, alphasort);
+  for (int i = 0; i < num_files; ++i) {
+    string curr_file = files[i]->d_name;
+    if (!isdigit(curr_file.at(0))) continue;
+    load_permanently(dir+'/'+curr_file);
+    free(files[i]);
+    files[i] = NULL;
+  }
+  free(files);
+}
+:(before "End Includes")
+#include<dirent.h>
+#include<sys/stat.h>
+
+//:: Reading from memory, writing to memory.
+
+:(code)
+vector<double> read_memory(reagent x) {
+  vector<double> result;
+  if (is_literal(x)) {
+    result.push_back(x.value);
+    return result;
+  }
+  long long int base = x.value;
+  long long int size = size_of(x);
+  for (long long int offset = 0; offset < size; ++offset) {
+    double val = Memory[base+offset];
+    trace(Primitive_recipe_depth, "mem") << "location " << base+offset << " is " << no_scientific(val) << end();
+    result.push_back(val);
+  }
+  return result;
+}
+
+void write_memory(reagent x, vector<double> data) {
+  if (is_dummy(x)) return;
+  if (is_literal(x)) return;
+  long long int base = x.value;
+  if (size_mismatch(x, data)) {
+    raise << current_recipe_name() << ": size mismatch in storing to " << x.original_string << " (" << size_of(x.types) << " vs " << SIZE(data) << ") at '" << current_instruction().to_string() << "'\n" << end();
+    return;
+  }
+  for (long long int offset = 0; offset < SIZE(data); ++offset) {
+    trace(Primitive_recipe_depth, "mem") << "storing " << no_scientific(data.at(offset)) << " in location " << base+offset << end();
+    Memory[base+offset] = data.at(offset);
+  }
+}
+
+:(code)
+long long int size_of(const reagent& r) {
+  if (r.types.empty()) return 0;
+  // End size_of(reagent) Cases
+  return size_of(r.types);
+}
+long long int size_of(const vector<type_ordinal>& types) {
+  if (types.empty()) return 0;
+  // End size_of(types) Cases
+  return 1;
+}
+
+bool size_mismatch(const reagent& x, const vector<double>& data) {
+  if (x.types.empty()) return true;
+  // End size_mismatch(x) Cases
+//?   if (size_of(x) != SIZE(data)) cerr << size_of(x) << " vs " << SIZE(data) << '\n';
+  return size_of(x) != SIZE(data);
+}
+
+bool is_dummy(const reagent& x) {
+  return x.name == "_";
+}
+
+:(replace{} "void run(string form)")
+// helper for tests
+void run(string form) {
+  vector<recipe_ordinal> tmp = load(form);
+  transform_all();
+  if (tmp.empty()) return;
+  run(tmp.front());
+}
+
+:(scenario run_label)
+recipe main [
+  +foo
+  1:number <- copy 23
+  2:number <- copy 1:number
+]
++run: 1:number <- copy 23
++run: 2:number <- copy 1:number
+-run: +foo
+
+:(scenario run_dummy)
+recipe main [
+  _ <- copy 0
+]
++run: _ <- copy 0
+
+:(scenario write_to_0_disallowed)
+recipe main [
+  0 <- copy 34
+]
+-mem: storing 34 in location 0
+
+//: mu is robust to various combinations of commas and spaces. You just have
+//: to put spaces around the '<-'.
+
+:(scenario comma_without_space)
+recipe main [
+  1:number, 2:number <- copy 2,2
+]
++mem: storing 2 in location 1
+
+:(scenario space_without_comma)
+recipe main [
+  1:number, 2:number <- copy 2 2
+]
++mem: storing 2 in location 1
+
+:(scenario comma_before_space)
+recipe main [
+  1:number, 2:number <- copy 2, 2
+]
++mem: storing 2 in location 1
+
+:(scenario comma_after_space)
+recipe main [
+  1:number, 2:number <- copy 2 ,2
+]
++mem: storing 2 in location 1