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+//: Phase 3: Start running a loaded and transformed recipe.
+//:
+//:   The process of running Mu code:
+//:     load -> transform -> run
+//:
+//: 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.
+
+void test_copy_literal() {
+  run(
+      "def main [\n"
+      "  1:num <- copy 23\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "run: {1: \"number\"} <- copy {23: \"literal\"}\n"
+      "mem: storing 23 in location 1\n"
+  );
+}
+
+void test_copy() {
+  run(
+      "def main [\n"
+      "  1:num <- copy 23\n"
+      "  2:num <- copy 1:num\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "run: {2: \"number\"} <- copy {1: \"number\"}\n"
+      "mem: location 1 is 23\n"
+      "mem: storing 23 in location 2\n"
+  );
+}
+
+void test_copy_multiple() {
+  run(
+      "def main [\n"
+      "  1:num, 2:num <- copy 23, 24\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "mem: storing 23 in location 1\n"
+      "mem: storing 24 in location 2\n"
+  );
+}
+
+:(before "End Types")
+// Book-keeping while running a recipe.
+//: Later layers will replace this to support running multiple routines at once.
+struct routine {
+  recipe_ordinal running_recipe;
+  int running_step_index;
+  routine(recipe_ordinal r) :running_recipe(r), running_step_index(0) {}
+  bool completed() const;
+  const vector<instruction>& steps() const;
+};
+
+:(before "End Globals")
+routine* Current_routine = NULL;
+:(before "End Reset")
+Current_routine = NULL;
+
+:(code)
+void run(const recipe_ordinal r) {
+  routine rr(r);
+  Current_routine = &rr;
+  run_current_routine();
+  Current_routine = NULL;
+}
+
+void run_current_routine() {
+  while (should_continue_running(Current_routine)) {  // beware: may modify Current_routine
+    // Running One Instruction
+    if (current_instruction().is_label) { ++current_step_index();  continue; }
+    trace(Callstack_depth, "run") << to_string(current_instruction()) << end();
+//?     if (Foo) cerr << "run: " << to_string(current_instruction()) << '\n';
+    if (get_or_insert(Memory, 0) != 0) {
+      raise << "something wrote to location 0; this should never happen\n" << end();
+      put(Memory, 0, 0);
+    }
+    // read all ingredients from memory, each potentially spanning multiple locations
+    vector<vector<double> > ingredients;
+    if (should_copy_ingredients()) {
+      for (int i = 0;  i < SIZE(current_instruction().ingredients);  ++i)
+        ingredients.push_back(read_memory(current_instruction().ingredients.at(i)));
+    }
+    // instructions below will write to 'products'
+    vector<vector<double> > products;
+    //: This will be a large switch that later layers will often insert cases
+    //: into. Never call 'continue' within it. Instead, we'll explicitly
+    //: control which of the following stages after the switch we run for each
+    //: instruction.
+    bool write_products = true;
+    bool fall_through_to_next_instruction = true;
+    switch (current_instruction().operation) {
+      // Primitive Recipe Implementations
+      case COPY: {
+        copy(ingredients.begin(), ingredients.end(), inserter(products, products.begin()));
+        break;
+      }
+      // End Primitive Recipe Implementations
+      default: {
+        raise << "not a primitive op: " << current_instruction().operation << '\n' << end();
+      }
+    }
+    //: used by a later layer
+    if (write_products) {
+      if (SIZE(products) < SIZE(current_instruction().products)) {
+        raise << SIZE(products) << " vs " << SIZE(current_instruction().products) << ": failed to write to all products in '" << to_original_string(current_instruction()) << "'\n" << end();
+      }
+      else {
+        for (int i = 0;  i < SIZE(current_instruction().products);  ++i) {
+          // Writing Instruction Product(i)
+          write_memory(current_instruction().products.at(i), products.at(i));
+        }
+      }
+    }
+    // End Running One Instruction
+    if (fall_through_to_next_instruction)
+      ++current_step_index();
+  }
+  stop_running_current_routine:;
+}
+
+//: Helpers for managing trace depths
+//:
+//: We're going to use trace depths primarily to segment code running at
+//: different frames of the call stack. This will make it easy for the trace
+//: browser to collapse over entire calls.
+//:
+//: The entire map of possible depths is as follows:
+//:
+//: Errors will be depth 0.
+//: Mu 'applications' will be able to use depths 1-99 as they like.
+//: Primitive statements will occupy 100 and up to Max_depth, organized by
+//: stack frames.
+:(before "End Globals")
+extern const int Initial_callstack_depth = 100;
+int Callstack_depth = Initial_callstack_depth;
+:(before "End Reset")
+Callstack_depth = Initial_callstack_depth;
+
+//: Other helpers for the VM.
+
+:(code)
+//: hook replaced in a later layer
+bool should_continue_running(const routine* current_routine) {
+  assert(current_routine == Current_routine);  // argument passed in just to make caller readable above
+  return !Current_routine->completed();
+}
+
+bool should_copy_ingredients() {
+  // End should_copy_ingredients Special-cases
+  return true;
+}
+
+bool is_mu_scalar(reagent/*copy*/ r) {
+  return is_mu_scalar(r.type);
+}
+bool is_mu_scalar(const type_tree* type) {
+  if (!type) return false;
+  if (is_mu_address(type)) return false;
+  if (!type->atom) return false;
+  if (is_literal(type))
+    return type->name != "literal-string";
+  return size_of(type) == 1;
+}
+
+bool is_mu_address(reagent/*copy*/ r) {
+  // End Preprocess is_mu_address(reagent r)
+  return is_mu_address(r.type);
+}
+bool is_mu_address(const type_tree* type) {
+  if (!type) return false;
+  if (is_literal(type)) return false;
+  if (type->atom) return false;
+  if (!type->left->atom) {
+    raise << "invalid type " << to_string(type) << '\n' << end();
+    return false;
+  }
+  return type->left->value == Address_type_ordinal;
+}
+
+//: Some helpers.
+//: Important that they return references into the current routine.
+
+//: hook replaced in a later layer
+int& current_step_index() {
+  return Current_routine->running_step_index;
+}
+
+//: hook replaced in a later layer
+recipe_ordinal currently_running_recipe() {
+  return Current_routine->running_recipe;
+}
+
+//: hook replaced in a later layer
+const string& current_recipe_name() {
+  return get(Recipe, Current_routine->running_recipe).name;
+}
+
+//: hook replaced in a later layer
+const recipe& current_recipe() {
+  return get(Recipe, Current_routine->running_recipe);
+}
+
+//: hook replaced in a later layer
+const instruction& current_instruction() {
+  return get(Recipe, Current_routine->running_recipe).steps.at(Current_routine->running_step_index);
+}
+
+//: hook replaced in a later layer
+bool routine::completed() const {
+  return running_step_index >= SIZE(get(Recipe, running_recipe).steps);
+}
+
+//: hook replaced in a later layer
+const vector<instruction>& routine::steps() const {
+  return get(Recipe, running_recipe).steps;
+}
+
+//:: Startup flow
+
+:(before "End Mu Prelude")
+load_file_or_directory("core.mu");
+//? DUMP("");
+//? exit(0);
+
+//: Step 2: load any .mu files provided at the commandline
+:(before "End Commandline Parsing")
+// Check For .mu Files
+if (argc > 1) {
+  // skip argv[0]
+  ++argv;
+  --argc;
+  while (argc > 0) {
+    // ignore argv past '--'; that's commandline args for 'main'
+    if (string(*argv) == "--") break;
+    if (starts_with(*argv, "--"))
+      cerr << "treating " << *argv << " as a file rather than an option\n";
+    load_file_or_directory(*argv);
+    --argc;
+    ++argv;
+  }
+  if (Run_tests) Recipe.erase(get(Recipe_ordinal, "main"));
+}
+transform_all();
+//? cerr << to_original_string(get(Type_ordinal, "editor")) << '\n';
+//? cerr << to_original_string(get(Recipe, get(Recipe_ordinal, "event-loop"))) << '\n';
+//? DUMP("");
+//? exit(0);
+if (trace_contains_errors()) return 1;
+if (Trace_stream && Run_tests) {
+  // We'll want a trace per test. Clear the trace.
+  delete Trace_stream;
+  Trace_stream = NULL;
+}
+save_snapshots();
+
+//: Step 3: if we aren't running tests, locate a recipe called 'main' and
+//: start running it.
+:(before "End Main")
+if (!Run_tests && contains_key(Recipe_ordinal, "main") && contains_key(Recipe, get(Recipe_ordinal, "main"))) {
+  // Running Main
+  reset();
+  trace(2, "run") << "=== Starting to run" << end();
+  assert(Num_calls_to_transform_all == 1);
+  run_main(argc, argv);
+}
+
+:(code)
+void run_main(int argc, char* argv[]) {
+  recipe_ordinal r = get(Recipe_ordinal, "main");
+  if (r) run(r);
+}
+
+void load_file_or_directory(string filename) {
+  if (is_directory(filename)) {
+    load_all(filename);
+    return;
+  }
+  ifstream fin(filename.c_str());
+  if (!fin) {
+    cerr << "no such file '" << filename << "'\n" << end();  // don't raise, just warn. just in case it's just a name for a test to run.
+    return;
+  }
+  trace(2, "load") << "=== " << filename << end();
+  load(fin);
+  fin.close();
+}
+
+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(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)) && ends_with(curr_file, ".mu"))
+      load_file_or_directory(dir+'/'+curr_file);
+    free(files[i]);
+    files[i] = NULL;
+  }
+  free(files);
+}
+
+bool ends_with(const string& s, const string& pat) {
+  for (string::const_reverse_iterator p = s.rbegin(), q = pat.rbegin();  q != pat.rend();  ++p, ++q) {
+    if (p == s.rend()) return false;  // pat too long
+    if (*p != *q) return false;
+  }
+  return true;
+}
+
+:(before "End Includes")
+#include <dirent.h>
+#include <sys/stat.h>
+
+//:: Reading from memory, writing to memory.
+
+:(code)
+vector<double> read_memory(reagent/*copy*/ x) {
+  // Begin Preprocess read_memory(x)
+  vector<double> result;
+  if (x.name == "null") result.push_back(/*alloc id*/0);
+  if (is_literal(x)) {
+    result.push_back(x.value);
+    return result;
+  }
+  // End Preprocess read_memory(x)
+  int size = size_of(x);
+  for (int offset = 0;  offset < size;  ++offset) {
+    double val = get_or_insert(Memory, x.value+offset);
+    trace(Callstack_depth+1, "mem") << "location " << x.value+offset << " is " << no_scientific(val) << end();
+    result.push_back(val);
+  }
+  return result;
+}
+
+void write_memory(reagent/*copy*/ x, const vector<double>& data) {
+  assert(Current_routine);  // run-time only
+  // Begin Preprocess write_memory(x, data)
+  if (!x.type) {
+    raise << "can't write to '" << to_string(x) << "'; no type\n" << end();
+    return;
+  }
+  if (is_dummy(x)) return;
+  if (is_literal(x)) return;
+  // End Preprocess write_memory(x, data)
+  if (x.value == 0) {
+    raise << "can't write to location 0 in '" << to_original_string(current_instruction()) << "'\n" << end();
+    return;
+  }
+  if (size_mismatch(x, data)) {
+    raise << maybe(current_recipe_name()) << "size mismatch in storing to '" << x.original_string << "' (" << size_of(x) << " vs " << SIZE(data) << ") at '" << to_original_string(current_instruction()) << "'\n" << end();
+    return;
+  }
+  // End write_memory(x) Special-cases
+  for (int offset = 0;  offset < SIZE(data);  ++offset) {
+    assert(x.value+offset > 0);
+    trace(Callstack_depth+1, "mem") << "storing " << no_scientific(data.at(offset)) << " in location " << x.value+offset << end();
+//?     if (Foo) cerr << "mem: storing " << no_scientific(data.at(offset)) << " in location " << x.value+offset << '\n';
+    put(Memory, x.value+offset, data.at(offset));
+  }
+}
+
+:(code)
+int size_of(const reagent& r) {
+  if (!r.type) return 0;
+  // End size_of(reagent r) Special-cases
+  return size_of(r.type);
+}
+int size_of(const type_tree* type) {
+  if (!type) return 0;
+  if (type->atom) {
+    if (type->value == -1) return 1;  // error value, but we'll raise it elsewhere
+    if (type->value == 0) return 1;
+    // End size_of(type) Atom Special-cases
+  }
+  else {
+    if (!type->left->atom) {
+      raise << "invalid type " << to_string(type) << '\n' << end();
+      return 0;
+    }
+    if (type->left->value == Address_type_ordinal) return 2;  // address and alloc id
+    // End size_of(type) Non-atom Special-cases
+  }
+  // End size_of(type) Special-cases
+  return 1;
+}
+
+bool size_mismatch(const reagent& x, const vector<double>& data) {
+  if (!x.type) return true;
+  // End size_mismatch(x) Special-cases
+//?   if (size_of(x) != SIZE(data)) cerr << size_of(x) << " vs " << SIZE(data) << '\n';
+  return size_of(x) != SIZE(data);
+}
+
+bool is_literal(const reagent& r) {
+  return is_literal(r.type);
+}
+bool is_literal(const type_tree* type) {
+  if (!type) return false;
+  if (!type->atom) return false;
+  return type->value == 0;
+}
+
+bool scalar(const vector<int>& x) {
+  return SIZE(x) == 1;
+}
+bool scalar(const vector<double>& x) {
+  return SIZE(x) == 1;
+}
+
+// helper for tests
+void run(const string& form) {
+  vector<recipe_ordinal> tmp = load(form);
+  transform_all();
+  if (tmp.empty()) return;
+  if (trace_contains_errors()) return;
+  // if a test defines main, it probably wants to start there regardless of
+  // definition order
+  if (contains_key(Recipe, get(Recipe_ordinal, "main")))
+    run(get(Recipe_ordinal, "main"));
+  else
+    run(tmp.front());
+}
+
+void test_run_label() {
+  run(
+      "def main [\n"
+      "  +foo\n"
+      "  1:num <- copy 23\n"
+      "  2:num <- copy 1:num\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "run: {1: \"number\"} <- copy {23: \"literal\"}\n"
+      "run: {2: \"number\"} <- copy {1: \"number\"}\n"
+  );
+  CHECK_TRACE_DOESNT_CONTAIN("run: +foo");
+}
+
+void test_run_dummy() {
+  run(
+      "def main [\n"
+      "  _ <- copy 0\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "run: _ <- copy {0: \"literal\"}\n"
+  );
+}
+
+void test_run_null() {
+  run(
+      "def main [\n"
+      "  1:&:num <- copy null\n"
+      "]\n"
+  );
+}
+
+void test_write_to_0_disallowed() {
+  Hide_errors = true;
+  run(
+      "def main [\n"
+      "  0:num <- copy 34\n"
+      "]\n"
+  );
+  CHECK_TRACE_DOESNT_CONTAIN("mem: storing 34 in location 0");
+}
+
+//: Mu is robust to various combinations of commas and spaces. You just have
+//: to put spaces around the '<-'.
+
+void test_comma_without_space() {
+  run(
+      "def main [\n"
+      "  1:num, 2:num <- copy 2,2\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "mem: storing 2 in location 1\n"
+  );
+}
+
+void test_space_without_comma() {
+  run(
+      "def main [\n"
+      "  1:num, 2:num <- copy 2 2\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "mem: storing 2 in location 1\n"
+  );
+}
+
+void test_comma_before_space() {
+  run(
+      "def main [\n"
+      "  1:num, 2:num <- copy 2, 2\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "mem: storing 2 in location 1\n"
+  );
+}
+
+void test_comma_after_space() {
+  run(
+      "def main [\n"
+      "  1:num, 2:num <- copy 2 ,2\n"
+      "]\n"
+  );
+  CHECK_TRACE_CONTENTS(
+      "mem: storing 2 in location 1\n"
+  );
+}
+
+//:: Counters for trying to understand where Mu programs are spending their
+//:: time.
+
+:(before "End Globals")
+bool Run_profiler = false;
+// We'll key profile information by recipe_ordinal rather than name because
+// it's more efficient, and because later layers will show more than just the
+// name of a recipe.
+//
+// One drawback: if you're clearing recipes your profile will be inaccurate.
+// So far that happens in tests, and in 'run-sandboxed' in a later layer.
+map<recipe_ordinal, int> Instructions_running;
+:(before "End Commandline Options(*arg)")
+else if (is_equal(*arg, "--profile")) {
+  Run_profiler = true;
+}
+:(after "Running One Instruction")
+if (Run_profiler) Instructions_running[currently_running_recipe()]++;
+:(before "End One-time Setup")
+atexit(dump_profile);
+:(code)
+void dump_profile() {
+  if (!Run_profiler) return;
+  if (Run_tests) {
+    cerr << "It's not a good idea to profile a run with tests, since tests can create conflicting recipes and mislead you. To try it anyway, comment out this check in the code.\n";
+    return;
+  }
+  ofstream fout;
+  fout.open("profile.instructions");
+  if (fout) {
+    for (map<recipe_ordinal, int>::iterator p = Instructions_running.begin();  p != Instructions_running.end();  ++p) {
+      fout << std::setw(9) << p->second << ' ' << header_label(p->first) << '\n';
+    }
+  }
+  fout.close();
+  // End dump_profile
+}
+
+// overridden in a later layer
+string header_label(const recipe_ordinal r) {
+  return get(Recipe, r).name;
+}