AssemblyScript
diff --git a/cli/asc.d.ts b/cli/asc.d.ts
@@ -56,7 +56,7 @@ export interface MemoryStream extends OutputStream {
 }
 
 /** Compiler options. */
-interface CompilerOptions {
+export interface CompilerOptions {
   /** Prints just the compiler's version and exits. */
   version?: boolean;
   /** Prints the help message and exits. */
@@ -146,7 +146,7 @@ interface CompilerOptions {
 }
 
 /** Compiler API options. */
-interface APIOptions {
+export interface APIOptions {
   /** Standard output stream to use. */
   stdout?: OutputStream;
   /** Standard error stream to use. */

diff --git a/cli/asc.js b/cli/asc.js
@@ -193,8 +193,9 @@ exports.main = function main(argv, options, callback) {
   if (!stdout) throw Error("'options.stdout' must be specified");
   if (!stderr) throw Error("'options.stderr' must be specified");
 
-  const opts = optionsUtil.parse(argv, exports.options);
-  let args = opts.options;
+  const opts = optionsUtil.parse(argv, exports.options, false);
+  let args = optionsUtil.addDefaults(exports.options, opts.options);
+  let cliArgs = opts.options;
 
   argv = opts.arguments;
   if (args.noColors) {
@@ -280,11 +281,14 @@ exports.main = function main(argv, options, callback) {
   const seenAsconfig = new Set();
   seenAsconfig.add(path.join(baseDir, args.config));
 
+  // First find all parent configs and add them each to the front
+  let entries = new Set();
   while (asconfig) {
-    // merge target first, then merge options, then merge extended asconfigs
+    // First merge targets
     if (asconfig.targets && asconfig.targets[target]) {
-      args = optionsUtil.merge(exports.options, asconfig.targets[target], args);
+      cliArgs = optionsUtil.merge(exports.options, cliArgs, asconfig.targets[target]);
     }
+
     if (asconfig.options) {
       if (asconfig.options.transform) {
         // ensure that a transform's path is relative to the current config
@@ -298,22 +302,20 @@ exports.main = function main(argv, options, callback) {
           return p;
         });
       }
-      args = optionsUtil.merge(exports.options, args, asconfig.options);
+      cliArgs = optionsUtil.merge(exports.options, cliArgs, asconfig.options);
     }
-
+    
     // entries are added to the compilation
     if (asconfig.entries) {
       for (const entry of asconfig.entries) {
-        argv.push(
-          path.isAbsolute(entry)
+        entries.add(
+          path.relative(baseDir, path.isAbsolute(entry)
             ? entry
             // the entry is relative to the asconfig directory
             : path.join(asconfigDir, entry)
-        );
+          ));
       }
     }
-
-    // asconfig "extends" another config, merging options of it's parent
     if (asconfig.extends) {
       asconfigDir = path.isAbsolute(asconfig.extends)
         // absolute extension path means we know the exact directory and location
@@ -329,12 +331,17 @@ exports.main = function main(argv, options, callback) {
         asconfig = getAsconfig(fileName, asconfigDir, readFile);
       }
     } else {
-      asconfig = null; // finished resolving the configuration chain
+      break;
     }
   }
+  // Merge in cli args
+  args = optionsUtil.merge(exports.options, cliArgs, args);
+  // Add entries
+  argv = argv.concat(Array.from(entries));
 
   // If showConfig print args and exit
   if (args.showConfig) {
+    args.argv = argv;
     stderr.write(JSON.stringify(args, null, 2));
     return callback(null);
   }

diff --git a/cli/util/options.js b/cli/util/options.js
@@ -31,7 +31,7 @@ function parse(argv, config, propagateDefaults = true) {
       if (typeof option.alias === "string") aliases[option.alias] = key;
       else if (Array.isArray(option.alias)) option.alias.forEach(alias => aliases[alias] = key);
     }
-    if (option.default != null) options[key] = option.default;
+    if (option.default != null && propagateDefaults) options[key] = option.default;
   });
 
   // iterate over argv
@@ -87,7 +87,9 @@ function parse(argv, config, propagateDefaults = true) {
     } else unknown.push(arg);
   }
   while (i < k) trailing.push(argv[i++]); // trailing
-  if (propagateDefaults) addDefaults(config, options);
+  if (propagateDefaults) {
+    options = addDefaults(config, options);
+  }
 
   return { options, unknown, arguments: args, trailing };
 }
@@ -224,12 +226,17 @@ exports.merge = merge;
 
 /** Populates default values on a parsed options result. */
 function addDefaults(config, options) {
+  const newOptions = {};
   for (const [key, { default: defaultValue }] of Object.entries(config)) {
-    if (options[key] == null && defaultValue != null) {
-      options[key] = defaultValue;
+    if (options[key] == null) {
+      if (defaultValue != null) {
+        newOptions[key] = defaultValue;
+      }
+    } else {
+      newOptions[key] = options[key];
     }
   }
-  return options;
+  return newOptions;
 }
 
 exports.addDefaults = addDefaults;
diff --git a/tests/asconfig/complicated/assembly/index.ts b/tests/asconfig/complicated/assembly/index.ts
@@ -1,6 +1,6 @@
-assert(ASC_OPTIMIZE_LEVEL == 3);
-assert(ASC_SHRINK_LEVEL == 1);
-assert(ASC_FEATURE_SIMD);
+assert(ASC_OPTIMIZE_LEVEL == 3, "expected optimize level == 3");
+assert(ASC_SHRINK_LEVEL == 1, "expected shrink level == 1");
+assert(ASC_FEATURE_SIMD, "expected SIMD enabled");
 let size = memory.size();
 trace("size", 1, size);
-assert(size == 30);
+assert(size == 30, "expected 30 got " + size.toString());
diff --git a/tests/asconfig/extends/asconfig.json b/tests/asconfig/extends/asconfig.json
@@ -5,7 +5,9 @@
     }
   },
   "options": {
-    "enable": ["simd"]
+    "enable": ["simd"],
+    "runtime": "half",
+    "noEmit": false
   },
   "extends": "./extends.json"
 }
diff --git a/tests/asconfig/extends/expected.json b/tests/asconfig/extends/expected.json
@@ -0,0 +1,6 @@
+{
+  "runtime": "half",
+  "noEmit": false,
+  "noAssert": true,
+  "enable": ["simd"]
+}
diff --git a/tests/asconfig/extends/extends.json b/tests/asconfig/extends/extends.json
@@ -6,6 +6,8 @@
     }
   },
   "options": {
-    "disable": ["simd"]
+    "disable": ["simd"],
+    "noEmit": true,
+    "noAssert": true
   }
 }
diff --git a/tests/asconfig/extends/package.json b/tests/asconfig/extends/package.json
@@ -1,6 +1,6 @@
 {
   "private": true,
   "scripts": {
-    "test": "node ../index.js"
+    "test": "node ../index.js --showConfig && node ../index.js"
   }
 }
diff --git a/tests/asconfig/index.js b/tests/asconfig/index.js
@@ -1,7 +1,11 @@
 const asc = require("../../cli/asc");
 const loader = require("../../lib/loader");
 const args = process.argv.slice(2);
+const path = require('path');
+const fs = require("fs");
 
+/** @type {string} */
+let stderr;
 /** @type {Uint8Array} */
 let binary;
 asc.main(["assembly/index.ts", "--outFile", "output.wasm", "--explicitStart", ...args], {
@@ -11,13 +15,51 @@ asc.main(["assembly/index.ts", "--outFile", "output.wasm", "--explicitStart", ..
     } else if (name !== "output.wasm.map") {
       throw Error("Unexpected output file: " + name);
     }
+  },
+  stderr: {
+    write(s) {
+      stderr = s;
+    }
   }
+
 }, (err) => {
   if (err) {
     console.error(err);
+    console.error(stderr);
     process.exit(1);
   }
 
+  const jsonPath = path.join(process.cwd(), "expected.json");
+  if (fs.existsSync(jsonPath) && stderr) {
+    const actual = JSON.parse(stderr);
+    const expected = require(jsonPath);
+    let errored = false;
+    for (let name of Object.getOwnPropertyNames(expected)) {
+      if (actual[name] !== expected[name]) {
+        // If object check just first level
+        if (typeof actual[name] === 'object' && typeof expected[name] === 'object') {
+          let error = false;
+          for (let field of Object.getOwnPropertyNames(actual[name])) {
+            if (actual[name][field] !== expected[name][field]) {
+              error = true;
+              break;
+            }
+          }
+          if (!error) {
+            continue;
+          }
+        }
+        console.error(name + ": " + actual[name] + " expected " + expected[name]);
+        errored = true;
+      }
+    }
+    if (errored) {
+      process.exit(1);
+    }
+    process.exit(0);
+  }
+
+
   if (!binary) {
     console.error("No binary was generated for the asconfig test in " + process.cwd());
     process.exit(1);
@@ -29,6 +71,7 @@ asc.main(["assembly/index.ts", "--outFile", "output.wasm", "--explicitStart", ..
     theModule.exports._start();
   } catch (err) {
     console.error("The wasm module _start() function failed in " + process.cwd());
+    console.error(err);
     process.exit(1);
   }
   return 0;

diff --git a/tests/asconfig/package.json b/tests/asconfig/package.json
@@ -1,12 +1,13 @@
 {
   "private": true,
   "scripts": {
-    "test": "npm run test:use-consts && npm run test:target && npm run test:entry-points && npm run test:complicated",
+    "test": "npm run test:use-consts && npm run test:target && npm run test:entry-points && npm run test:complicated && npm run test:extends",
     "test:use-consts": "cd use-consts && npm run test",
     "test:entry-points": "cd entry-points && npm run test",
     "test:respect-inheritence": "cd respect-inheritence && npm run test",
     "test:target": "cd target && npm run test",
     "test:cyclical": "cd cyclical && npm run test",
-    "test:complicated": "cd complicated && npm run test"
+    "test:complicated": "cd complicated && npm run test",
+    "test:extends": "cd extends && npm run test"
   }
 }
diff --git a/tests/asconfig/target/asconfig.json b/tests/asconfig/target/asconfig.json
@@ -9,5 +9,7 @@
       "debug": true
     }
   },
-  "options": {}
+  "options": {
+    "runtime": "stub"
+  }
 }
diff --git a/tests/asconfig/target/assembly/index.ts b/tests/asconfig/target/assembly/index.ts
@@ -1,3 +1,3 @@
-assert(ASC_OPTIMIZE_LEVEL == 3);
-assert(ASC_SHRINK_LEVEL == 1);
-assert(ASC_FEATURE_SIMD);
+assert(ASC_OPTIMIZE_LEVEL == 3, "expected optimize level == 3");
+assert(ASC_SHRINK_LEVEL == 1, "expected shrink level == 1");
+assert(ASC_FEATURE_SIMD, "expected SIMD enabled");
diff --git a/tests/asconfig/target/expected.json b/tests/asconfig/target/expected.json
@@ -0,0 +1,3 @@
+{
+  "runtime": "none"
+}
diff --git a/tests/asconfig/target/package.json b/tests/asconfig/target/package.json
@@ -1,6 +1,6 @@
 {
   "private": true,
   "scripts": {
-    "test": "node ../index.js"
+    "test": "node ../index.js --target && node ../index.js --showConfig --runtime none"
   }
 }