add "deno run" subcommand (#2215)

54 files changed, 314 insertions, 210 deletions

diff --git a/cli/flags.rs b/cli/flags.rs
index f60c1a3fa..6e690645b 100644
--- a/cli/flags.rs
+++ b/cli/flags.rs
@@ -36,75 +36,41 @@ pub fn create_cli_app<'a, 'b>() -> App<'a, 'b> {
   App::new("deno")
     .bin_name("deno")
     .global_settings(&[AppSettings::ColorNever])
-    .settings(&[
-      AppSettings::AllowExternalSubcommands,
-      AppSettings::DisableVersion,
-    ]).after_help(ENV_VARIABLES_HELP)
+    .settings(&[AppSettings::DisableVersion])
+    .after_help(ENV_VARIABLES_HELP)
     .arg(
-      Arg::with_name("allow-read")
-        .long("allow-read")
-        .help("Allow file system read access"),
-    ).arg(
-      Arg::with_name("allow-write")
-        .long("allow-write")
-        .help("Allow file system write access"),
-    ).arg(
-      Arg::with_name("allow-net")
-        .long("allow-net")
-        .help("Allow network access"),
-    ).arg(
-      Arg::with_name("allow-env")
-        .long("allow-env")
-        .help("Allow environment access"),
-    ).arg(
-      Arg::with_name("allow-run")
-        .long("allow-run")
-        .help("Allow running subprocesses"),
-    ).arg(
-      Arg::with_name("allow-high-precision")
-        .long("allow-high-precision")
-        .help("Allow high precision time measurement"),
-    ).arg(
-      Arg::with_name("allow-all")
-        .short("A")
-        .long("allow-all")
-        .help("Allow all permissions"),
-    ).arg(
-      Arg::with_name("no-prompt")
-        .long("no-prompt")
-        .help("Do not use prompts"),
-    ).arg(
-      Arg::with_name("no-fetch")
-        .long("no-fetch")
-        .help("Do not download remote modules"),
-    ).arg(
       Arg::with_name("log-debug")
         .short("D")
         .long("log-debug")
-        .help("Log debug output"),
+        .help("Log debug output")
+        .global(true),
     ).arg(
       Arg::with_name("reload")
         .short("r")
         .long("reload")
-        .help("Reload source code cache (recompile TypeScript)"),
+        .help("Reload source code cache (recompile TypeScript)")
+        .global(true),
     ).arg(
       Arg::with_name("config")
         .short("c")
         .long("config")
         .value_name("FILE")
         .help("Load compiler configuration file")
-        .takes_value(true),
+        .takes_value(true)
+        .global(true),
     ).arg(
       Arg::with_name("v8-options")
         .long("v8-options")
-        .help("Print V8 command line options"),
+        .help("Print V8 command line options")
+        .global(true),
     ).arg(
       Arg::with_name("v8-flags")
         .long("v8-flags")
         .takes_value(true)
         .use_delimiter(true)
         .require_equals(true)
-        .help("Set V8 command line options"),
+        .help("Set V8 command line options")
+        .global(true),
     ).subcommand(
       SubCommand::with_name("version")
         .setting(AppSettings::DisableVersion)
@@ -196,7 +162,69 @@ Prettier dependencies on first run.
             .required(true),
         ),
     ).subcommand(
-      SubCommand::with_name("xeval")
+      SubCommand::with_name("run")
+        .settings(&[
+          AppSettings::AllowExternalSubcommands,
+          AppSettings::DisableHelpSubcommand,
+          AppSettings::DisableVersion,
+          AppSettings::SubcommandRequired,
+        ]).about("Run a program given a filename or url to the source code")
+        .long_about(
+          "
+Run a program given a filename or url to the source code.
+
+By default all programs are run in sandbox without access to disk, network or
+ability to spawn subprocesses.
+
+  deno run https://deno.land/welcome.ts
+
+  # run program with permission to read from disk and listen to network
+  deno run --allow-net --allow-read https://deno.land/std/http/file_server.ts
+
+  # run program with all permissions
+  deno run -A https://deno.land/std/http/file_server.ts
+",
+        ).arg(
+          Arg::with_name("allow-read")
+            .long("allow-read")
+            .help("Allow file system read access"),
+        ).arg(
+          Arg::with_name("allow-write")
+            .long("allow-write")
+            .help("Allow file system write access"),
+        ).arg(
+          Arg::with_name("allow-net")
+            .long("allow-net")
+            .help("Allow network access"),
+        ).arg(
+          Arg::with_name("allow-env")
+            .long("allow-env")
+            .help("Allow environment access"),
+        ).arg(
+          Arg::with_name("allow-run")
+            .long("allow-run")
+            .help("Allow running subprocesses"),
+        ).arg(
+          Arg::with_name("allow-high-precision")
+            .long("allow-high-precision")
+            .help("Allow high precision time measurement"),
+        ).arg(
+          Arg::with_name("allow-all")
+            .short("A")
+            .long("allow-all")
+            .help("Allow all permissions"),
+        ).arg(
+          Arg::with_name("no-prompt")
+            .long("no-prompt")
+            .help("Do not use prompts"),
+        ).subcommand(
+          // this is a fake subcommand - it's used in conjunction with
+          // AppSettings:AllowExternalSubcommand to treat it as an
+          // entry point script
+          SubCommand::with_name("<script>").about("Script to run"),
+        ),
+    ).subcommand(
+    SubCommand::with_name("xeval")
         .setting(AppSettings::DisableVersion)
         .about("Eval a script on text segments from stdin")
         .long_about(
@@ -226,14 +254,8 @@ Otherwise '$' will be used as default variable name.
             .help("Set delimiter, defaults to newline")
             .takes_value(true),
         ).arg(Arg::with_name("code").takes_value(true).required(true)),
-    ).subcommand(
-      // this is a fake subcommand - it's used in conjunction with
-      // AppSettings:AllowExternalSubcommand to treat it as an
-      // entry point script
-      SubCommand::with_name("<script>").about("Script to run"),
     )
 }
-
 /// Parse ArgMatches into internal DenoFlags structure.
 /// This method should not make any side effects.
 #[cfg_attr(feature = "cargo-clippy", allow(stutter))]
@@ -250,39 +272,6 @@ pub fn parse_flags(matches: ArgMatches) -> DenoFlags {
     flags.reload = true;
   }
   flags.config_path = matches.value_of("config").map(ToOwned::to_owned);
-  if matches.is_present("allow-read") {
-    flags.allow_read = true;
-  }
-  if matches.is_present("allow-write") {
-    flags.allow_write = true;
-  }
-  if matches.is_present("allow-net") {
-    flags.allow_net = true;
-  }
-  if matches.is_present("allow-env") {
-    flags.allow_env = true;
-  }
-  if matches.is_present("allow-run") {
-    flags.allow_run = true;
-  }
-  if matches.is_present("allow-high-precision") {
-    flags.allow_high_precision = true;
-  }
-  if matches.is_present("allow-all") {
-    flags.allow_read = true;
-    flags.allow_env = true;
-    flags.allow_net = true;
-    flags.allow_run = true;
-    flags.allow_read = true;
-    flags.allow_write = true;
-    flags.allow_high_precision = true;
-  }
-  if matches.is_present("no-prompt") {
-    flags.no_prompts = true;
-  }
-  if matches.is_present("no-fetch") {
-    flags.no_fetch = true;
-  }
   if matches.is_present("v8-options") {
     let v8_flags = svec!["deno", "--help"];
     flags.v8_flags = Some(v8_flags);
@@ -298,6 +287,40 @@ pub fn parse_flags(matches: ArgMatches) -> DenoFlags {
     flags.v8_flags = Some(v8_flags);
   }
 
+  // flags specific to "run" subcommand
+  if let Some(run_matches) = matches.subcommand_matches("run") {
+    if run_matches.is_present("allow-read") {
+      flags.allow_read = true;
+    }
+    if run_matches.is_present("allow-write") {
+      flags.allow_write = true;
+    }
+    if run_matches.is_present("allow-net") {
+      flags.allow_net = true;
+    }
+    if run_matches.is_present("allow-env") {
+      flags.allow_env = true;
+    }
+    if run_matches.is_present("allow-run") {
+      flags.allow_run = true;
+    }
+    if run_matches.is_present("allow-high-precision") {
+      flags.allow_high_precision = true;
+    }
+    if run_matches.is_present("allow-all") {
+      flags.allow_read = true;
+      flags.allow_env = true;
+      flags.allow_net = true;
+      flags.allow_run = true;
+      flags.allow_read = true;
+      flags.allow_write = true;
+      flags.allow_high_precision = true;
+    }
+    if run_matches.is_present("no-prompt") {
+      flags.no_prompts = true;
+    }
+  }
+
   flags
 }
 
@@ -314,6 +337,7 @@ pub enum DenoSubcommand {
   Repl,
   Run,
   Types,
+  Version,
   Xeval,
 }
 
@@ -327,6 +351,12 @@ pub fn flags_from_vec(
 
   let subcommand = match matches.subcommand() {
     ("eval", Some(eval_match)) => {
+      flags.allow_net = true;
+      flags.allow_env = true;
+      flags.allow_run = true;
+      flags.allow_read = true;
+      flags.allow_write = true;
+      flags.allow_high_precision = true;
       let code: &str = eval_match.value_of("code").unwrap();
       argv.extend(vec![code.to_string()]);
       DenoSubcommand::Eval
@@ -356,6 +386,25 @@ pub fn flags_from_vec(
       DenoSubcommand::Info
     }
     ("types", Some(_)) => DenoSubcommand::Types,
+    ("run", Some(run_match)) => {
+      match run_match.subcommand() {
+        (script, Some(script_match)) => {
+          argv.extend(vec![script.to_string()]);
+          // check if there are any extra arguments that should
+          // be passed to script
+          if script_match.is_present("") {
+            let script_args: Vec<String> = script_match
+              .values_of("")
+              .unwrap()
+              .map(String::from)
+              .collect();
+            argv.extend(script_args);
+          }
+          DenoSubcommand::Run
+        }
+        _ => unreachable!(),
+      }
+    }
     ("xeval", Some(eval_match)) => {
       let code: &str = eval_match.value_of("code").unwrap();
       flags.xeval_replvar =
@@ -367,21 +416,16 @@ pub fn flags_from_vec(
       argv.extend(vec![code.to_string()]);
       DenoSubcommand::Xeval
     }
-    (script, Some(script_match)) => {
-      argv.extend(vec![script.to_string()]);
-      // check if there are any extra arguments that should
-      // be passed to script
-      if script_match.is_present("") {
-        let script_args: Vec<String> = script_match
-          .values_of("")
-          .unwrap()
-          .map(String::from)
-          .collect();
-        argv.extend(script_args);
-      }
-      DenoSubcommand::Run
+    ("version", Some(_)) => DenoSubcommand::Version,
+    _ => {
+      flags.allow_net = true;
+      flags.allow_env = true;
+      flags.allow_run = true;
+      flags.allow_read = true;
+      flags.allow_write = true;
+      flags.allow_high_precision = true;
+      DenoSubcommand::Repl
     }
-    _ => DenoSubcommand::Repl,
   };
 
   (flags, subcommand, argv)
@@ -401,14 +445,14 @@ mod tests {
         ..DenoFlags::default()
       }
     );
-    assert_eq!(subcommand, DenoSubcommand::Run);
-    assert_eq!(argv, svec!["deno", "version"]);
+    assert_eq!(subcommand, DenoSubcommand::Version);
+    assert_eq!(argv, svec!["deno"]);
   }
 
   #[test]
   fn test_flags_from_vec_2() {
     let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "-r", "-D", "script.ts"]);
+      flags_from_vec(svec!["deno", "-r", "-D", "run", "script.ts"]);
     assert_eq!(
       flags,
       DenoFlags {
@@ -423,12 +467,19 @@ mod tests {
 
   #[test]
   fn test_flags_from_vec_3() {
-    let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "-r", "--allow-write", "script.ts"]);
+    let (flags, subcommand, argv) = flags_from_vec(svec![
+      "deno",
+      "run",
+      "-r",
+      "-D",
+      "--allow-write",
+      "script.ts"
+    ]);
     assert_eq!(
       flags,
       DenoFlags {
         reload: true,
+        log_debug: true,
         allow_write: true,
         ..DenoFlags::default()
       }
@@ -440,7 +491,7 @@ mod tests {
   #[test]
   fn test_flags_from_vec_4() {
     let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "-Dr", "--allow-write", "script.ts"]);
+      flags_from_vec(svec!["deno", "-Dr", "run", "--allow-write", "script.ts"]);
     assert_eq!(
       flags,
       DenoFlags {
@@ -457,7 +508,7 @@ mod tests {
   #[test]
   fn test_flags_from_vec_5() {
     let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "--v8-options"]);
+      flags_from_vec(svec!["deno", "--v8-options", "run", "script.ts"]);
     assert_eq!(
       flags,
       DenoFlags {
@@ -465,11 +516,15 @@ mod tests {
         ..DenoFlags::default()
       }
     );
-    assert_eq!(subcommand, DenoSubcommand::Repl);
-    assert_eq!(argv, svec!["deno"]);
+    assert_eq!(subcommand, DenoSubcommand::Run);
+    assert_eq!(argv, svec!["deno", "script.ts"]);
 
-    let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "--v8-flags=--expose-gc,--gc-stats=1"]);
+    let (flags, subcommand, argv) = flags_from_vec(svec![
+      "deno",
+      "--v8-flags=--expose-gc,--gc-stats=1",
+      "run",
+      "script.ts"
+    ]);
     assert_eq!(
       flags,
       DenoFlags {
@@ -477,14 +532,20 @@ mod tests {
         ..DenoFlags::default()
       }
     );
-    assert_eq!(subcommand, DenoSubcommand::Repl);
-    assert_eq!(argv, svec!["deno"]);
+    assert_eq!(subcommand, DenoSubcommand::Run);
+    assert_eq!(argv, svec!["deno", "script.ts"]);
   }
 
   #[test]
   fn test_flags_from_vec_6() {
-    let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "--allow-net", "gist.ts", "--title", "X"]);
+    let (flags, subcommand, argv) = flags_from_vec(svec![
+      "deno",
+      "run",
+      "--allow-net",
+      "gist.ts",
+      "--title",
+      "X"
+    ]);
     assert_eq!(
       flags,
       DenoFlags {
@@ -499,7 +560,7 @@ mod tests {
   #[test]
   fn test_flags_from_vec_7() {
     let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "--allow-all", "gist.ts"]);
+      flags_from_vec(svec!["deno", "run", "--allow-all", "gist.ts"]);
     assert_eq!(
       flags,
       DenoFlags {
@@ -519,7 +580,7 @@ mod tests {
   #[test]
   fn test_flags_from_vec_8() {
     let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "--allow-read", "gist.ts"]);
+      flags_from_vec(svec!["deno", "run", "--allow-read", "gist.ts"]);
     assert_eq!(
       flags,
       DenoFlags {
@@ -533,8 +594,12 @@ mod tests {
 
   #[test]
   fn test_flags_from_vec_9() {
-    let (flags, subcommand, argv) =
-      flags_from_vec(svec!["deno", "--allow-high-precision", "script.ts"]);
+    let (flags, subcommand, argv) = flags_from_vec(svec![
+      "deno",
+      "run",
+      "--allow-high-precision",
+      "script.ts"
+    ]);
     assert_eq!(
       flags,
       DenoFlags {
@@ -553,6 +618,7 @@ mod tests {
     // script args as Deno.args
     let (flags, subcommand, argv) = flags_from_vec(svec![
       "deno",
+      "run",
       "--allow-write",
       "script.ts",
       "-D",
@@ -616,6 +682,60 @@ mod tests {
 
   #[test]
   fn test_flags_from_vec_15() {
+    let (flags, subcommand, argv) =
+      flags_from_vec(svec!["deno", "run", "-c", "tsconfig.json", "script.ts"]);
+    assert_eq!(
+      flags,
+      DenoFlags {
+        config_path: Some("tsconfig.json".to_owned()),
+        ..DenoFlags::default()
+      }
+    );
+    assert_eq!(subcommand, DenoSubcommand::Run);
+    assert_eq!(argv, svec!["deno", "script.ts"]);
+  }
+
+  #[test]
+  fn test_flags_from_vec_16() {
+    let (flags, subcommand, argv) =
+      flags_from_vec(svec!["deno", "eval", "'console.log(\"hello\")'"]);
+    assert_eq!(
+      flags,
+      DenoFlags {
+        allow_net: true,
+        allow_env: true,
+        allow_run: true,
+        allow_read: true,
+        allow_write: true,
+        allow_high_precision: true,
+        ..DenoFlags::default()
+      }
+    );
+    assert_eq!(subcommand, DenoSubcommand::Eval);
+    assert_eq!(argv, svec!["deno", "'console.log(\"hello\")'"]);
+  }
+
+  #[test]
+  fn test_flags_from_vec_17() {
+    let (flags, subcommand, argv) = flags_from_vec(svec!["deno"]);
+    assert_eq!(
+      flags,
+      DenoFlags {
+        allow_net: true,
+        allow_env: true,
+        allow_run: true,
+        allow_read: true,
+        allow_write: true,
+        allow_high_precision: true,
+        ..DenoFlags::default()
+      }
+    );
+    assert_eq!(subcommand, DenoSubcommand::Repl);
+    assert_eq!(argv, svec!["deno"]);
+  }
+
+  #[test]
+  fn test_flags_from_vec_18() {
     let (flags, subcommand, argv) = flags_from_vec(svec![
       "deno",
       "xeval",
@@ -632,17 +752,4 @@ mod tests {
     assert_eq!(subcommand, DenoSubcommand::Xeval);
     assert_eq!(argv, svec!["deno", "console.log(val)"]);
   }
-
-  #[test]
-  fn test_set_flags_11() {
-    let (flags, _, _) =
-      flags_from_vec(svec!["deno", "-c", "tsconfig.json", "script.ts"]);
-    assert_eq!(
-      flags,
-      DenoFlags {
-        config_path: Some("tsconfig.json".to_owned()),
-        ..DenoFlags::default()
-      }
-    )
-  }
 }
diff --git a/cli/main.rs b/cli/main.rs
index 5a6efa073..8bef2d2ff 100644
--- a/cli/main.rs
+++ b/cli/main.rs
@@ -300,6 +300,7 @@ fn main() {
     DenoSubcommand::Repl => run_repl(flags, argv),
     DenoSubcommand::Run => run_script(flags, argv),
     DenoSubcommand::Types => types_command(),
+    DenoSubcommand::Version => run_script(flags, argv),
     DenoSubcommand::Xeval => xeval_command(flags, argv),
   }
 }
diff --git a/tests/001_hello.test b/tests/001_hello.test
index 121dbb2ea..27cc21f33 100644
--- a/tests/001_hello.test
+++ b/tests/001_hello.test
@@ -1,2 +1,2 @@
-args: --reload tests/001_hello.js
+args: run --reload tests/001_hello.js
 output: tests/001_hello.js.out
diff --git a/tests/002_hello.test b/tests/002_hello.test
index d889acd00..412b2ac79 100644
--- a/tests/002_hello.test
+++ b/tests/002_hello.test
@@ -1,2 +1,2 @@
-args: --reload tests/002_hello.ts
+args: run --reload tests/002_hello.ts
 output: tests/002_hello.ts.out
diff --git a/tests/003_relative_import.test b/tests/003_relative_import.test
index 5206c1aaa..0f69633e0 100644
--- a/tests/003_relative_import.test
+++ b/tests/003_relative_import.test
@@ -1,2 +1,2 @@
-args: --reload tests/003_relative_import.ts
+args: run --reload tests/003_relative_import.ts
 output: tests/003_relative_import.ts.out
diff --git a/tests/004_set_timeout.test b/tests/004_set_timeout.test
index 6fda34f25..e4a534f48 100644
--- a/tests/004_set_timeout.test
+++ b/tests/004_set_timeout.test
@@ -1,2 +1,2 @@
-args: --reload tests/004_set_timeout.ts
+args: run --reload tests/004_set_timeout.ts
 output: tests/004_set_timeout.ts.out
diff --git a/tests/005_more_imports.test b/tests/005_more_imports.test
index fde5276fe..3bc2e999d 100644
--- a/tests/005_more_imports.test
+++ b/tests/005_more_imports.test
@@ -1,2 +1,2 @@
-args: --reload tests/005_more_imports.ts
+args: run --reload tests/005_more_imports.ts
 output: tests/005_more_imports.ts.out
diff --git a/tests/006_url_imports.test b/tests/006_url_imports.test
index 13c04219a..28d9116f7 100644
--- a/tests/006_url_imports.test
+++ b/tests/006_url_imports.test
@@ -1,2 +1,2 @@
-args: --reload tests/006_url_imports.ts
+args: run --reload tests/006_url_imports.ts
 output: tests/006_url_imports.ts.out
diff --git a/tests/012_async.test b/tests/012_async.test
index 3694d7362..63a0e0d23 100644
--- a/tests/012_async.test
+++ b/tests/012_async.test
@@ -1,2 +1,2 @@
-args: --reload tests/012_async.ts
+args: run --reload tests/012_async.ts
 output: tests/012_async.ts.out
diff --git a/tests/016_double_await.test b/tests/016_double_await.test
index 842d167cc..a1448e5a1 100644
--- a/tests/016_double_await.test
+++ b/tests/016_double_await.test
@@ -1,2 +1,2 @@
-args: --allow-read --reload tests/016_double_await.ts
+args: run --allow-read --reload tests/016_double_await.ts
 output: tests/016_double_await.ts.out
diff --git a/tests/017_import_redirect.test b/tests/017_import_redirect.test
index db7439f05..d8e7570db 100644
--- a/tests/017_import_redirect.test
+++ b/tests/017_import_redirect.test
@@ -1,2 +1,2 @@
-args: --reload tests/017_import_redirect.ts
+args: run --reload tests/017_import_redirect.ts
 output: tests/017_import_redirect.ts.out
diff --git a/tests/018_async_catch.test b/tests/018_async_catch.test
index 08961916d..ee62836ab 100644
--- a/tests/018_async_catch.test
+++ b/tests/018_async_catch.test
@@ -1,2 +1,2 @@
-args: --reload tests/018_async_catch.ts
+args: run --reload tests/018_async_catch.ts
 output: tests/018_async_catch.ts.out
diff --git a/tests/019_media_types.test b/tests/019_media_types.test
index c0fea5bc6..d311abc10 100644
--- a/tests/019_media_types.test
+++ b/tests/019_media_types.test
@@ -1,2 +1,2 @@
-args: --reload tests/019_media_types.ts
+args: run --reload tests/019_media_types.ts
 output: tests/019_media_types.ts.out
diff --git a/tests/020_json_modules.test b/tests/020_json_modules.test
index cacd21da0..624d69db3 100644
--- a/tests/020_json_modules.test
+++ b/tests/020_json_modules.test
@@ -1,2 +1,2 @@
-args: --reload tests/020_json_modules.ts
+args: run --reload tests/020_json_modules.ts
 output: tests/020_json_modules.ts.out
diff --git a/tests/021_mjs_modules.test b/tests/021_mjs_modules.test
index 9b60b9d97..b74554fb1 100644
--- a/tests/021_mjs_modules.test
+++ b/tests/021_mjs_modules.test
@@ -1,2 +1,2 @@
-args: --reload tests/021_mjs_modules.ts
+args: run --reload tests/021_mjs_modules.ts
 output: tests/021_mjs_modules.ts.out
diff --git a/tests/023_no_ext_with_headers.test b/tests/023_no_ext_with_headers.test
index b663f174c..cbab7cabd 100644
--- a/tests/023_no_ext_with_headers.test
+++ b/tests/023_no_ext_with_headers.test
@@ -1,2 +1,2 @@
-args: --reload tests/023_no_ext_with_headers
+args: run --reload tests/023_no_ext_with_headers
 output: tests/023_no_ext_with_headers.out
diff --git a/tests/024_import_no_ext_with_headers.test b/tests/024_import_no_ext_with_headers.test
index efaca96c3..e76a9d5ac 100644
--- a/tests/024_import_no_ext_with_headers.test
+++ b/tests/024_import_no_ext_with_headers.test
@@ -1,2 +1,2 @@
-args: --reload tests/024_import_no_ext_with_headers.ts
+args: run --reload tests/024_import_no_ext_with_headers.ts
 output: tests/024_import_no_ext_with_headers.ts.out
diff --git a/tests/025_high_precision.test b/tests/025_high_precision.test
index 2bc460c9b..fbdbbe8f9 100644
--- a/tests/025_high_precision.test
+++ b/tests/025_high_precision.test
@@ -1,2 +1,2 @@
-args: --allow-high-precision --reload tests/025_high_precision.ts
+args: run --allow-high-precision --reload tests/025_high_precision.ts
 output: tests/025_high_precision.ts.out
diff --git a/tests/025_reload_js_type_error.test b/tests/025_reload_js_type_error.test
index a2cd214be..d88c1c578 100644
--- a/tests/025_reload_js_type_error.test
+++ b/tests/025_reload_js_type_error.test
@@ -1,2 +1,2 @@
-args: --reload tests/025_reload_js_type_error.js
+args: run --reload tests/025_reload_js_type_error.js
 output: tests/025_reload_js_type_error.js.out
diff --git a/tests/026_redirect_javascript.js.test b/tests/026_redirect_javascript.js.test
index 81d0ad038..2b1f0d522 100644
--- a/tests/026_redirect_javascript.js.test
+++ b/tests/026_redirect_javascript.js.test
@@ -1,2 +1,2 @@
-args: --reload tests/026_redirect_javascript.js
+args: run --reload tests/026_redirect_javascript.js
 output: tests/026_redirect_javascript.js.out
diff --git a/tests/026_workers.test b/tests/026_workers.test
index 5019a9256..1d973a6c5 100644
--- a/tests/026_workers.test
+++ b/tests/026_workers.test
@@ -1,2 +1,2 @@
-args: --reload tests/026_workers.ts
+args: run --reload tests/026_workers.ts
 output: tests/026_workers.ts.out
diff --git a/tests/027_redirect_typescript.ts.test b/tests/027_redirect_typescript.ts.test
index 8762e61f2..ba2525ff6 100644
--- a/tests/027_redirect_typescript.ts.test
+++ b/tests/027_redirect_typescript.ts.test
@@ -1,2 +1,2 @@
-args: --reload tests/027_redirect_typescript.ts
+args: run --reload tests/027_redirect_typescript.ts
 output: tests/027_redirect_typescript.ts.out
diff --git a/tests/028_args.test b/tests/028_args.test
index df3c56205..af98c8b7a 100644
--- a/tests/028_args.test
+++ b/tests/028_args.test
@@ -1,2 +1,2 @@
-args: --reload tests/028_args.ts --arg1 val1 --arg2=val2 -- arg3 arg4
+args: run --reload tests/028_args.ts --arg1 val1 --arg2=val2 -- arg3 arg4
 output: tests/028_args.ts.out
diff --git a/tests/async_error.test b/tests/async_error.test
index 8ebbfb56c..2cc8de922 100644
--- a/tests/async_error.test
+++ b/tests/async_error.test
@@ -1,4 +1,4 @@
 exit_code: 1
-args: --reload tests/async_error.ts
+args: run --reload tests/async_error.ts
 check_stderr: true
 output: tests/async_error.ts.out
diff --git a/tests/circular1.test b/tests/circular1.test
index d86a00c31..80afb035b 100644
--- a/tests/circular1.test
+++ b/tests/circular1.test
@@ -1,2 +1,2 @@
-args: tests/circular1.js --reload
+args: run --reload tests/circular1.js
 output: tests/circular1.js.out
diff --git a/tests/config.test b/tests/config.test
index ee811ab8b..d8c5fde99 100644
--- a/tests/config.test
+++ b/tests/config.test
@@ -1,4 +1,4 @@
-args: --reload --config tests/config.tsconfig.json tests/config.ts
+args: run --reload --config tests/config.tsconfig.json tests/config.ts
 check_stderr: true
 exit_code: 1
 output: tests/config.ts.out
diff --git a/tests/error_001.test b/tests/error_001.test
index ca0a2ef2e..df1ee5f4a 100644
--- a/tests/error_001.test
+++ b/tests/error_001.test
@@ -1,4 +1,4 @@
-args: --reload tests/error_001.ts
+args: run --reload tests/error_001.ts
 check_stderr: true
 exit_code: 1
 output: tests/error_001.ts.out
diff --git a/tests/error_002.test b/tests/error_002.test
index 12f6e3cec..d2954506d 100644
--- a/tests/error_002.test
+++ b/tests/error_002.test
@@ -1,4 +1,4 @@
-args: --reload tests/error_002.ts
+args: run --reload tests/error_002.ts
 check_stderr: true
 exit_code: 1
 output: tests/error_002.ts.out
diff --git a/tests/error_003_typescript.test b/tests/error_003_typescript.test
index 7a9d4a8ea..f721829a2 100644
--- a/tests/error_003_typescript.test
+++ b/tests/error_003_typescript.test
@@ -1,3 +1,3 @@
-args: --reload tests/error_003_typescript.ts
+args: run --reload tests/error_003_typescript.ts
 exit_code: 1
 output: tests/error_003_typescript.ts.out
diff --git a/tests/error_004_missing_module.test b/tests/error_004_missing_module.test
index b94c86004..99c25908c 100644
--- a/tests/error_004_missing_module.test
+++ b/tests/error_004_missing_module.test
@@ -1,4 +1,4 @@
-args: tests/error_004_missing_module.ts --reload
+args: run --reload tests/error_004_missing_module.ts
 check_stderr: true
 exit_code: 1
 output: tests/error_004_missing_module.ts.out
diff --git a/tests/error_005_missing_dynamic_import.test b/tests/error_005_missing_dynamic_import.test
index 2acf467c1..ffbf20be9 100644
--- a/tests/error_005_missing_dynamic_import.test
+++ b/tests/error_005_missing_dynamic_import.test
@@ -1,4 +1,4 @@
-args: tests/error_005_missing_dynamic_import.ts --reload
+args: run --reload tests/error_005_missing_dynamic_import.ts
 check_stderr: true
 exit_code: 1
 output: tests/error_005_missing_dynamic_import.ts.out
diff --git a/tests/error_006_import_ext_failure.test b/tests/error_006_import_ext_failure.test
index 5fe245739..59a82a364 100644
--- a/tests/error_006_import_ext_failure.test
+++ b/tests/error_006_import_ext_failure.test
@@ -1,4 +1,4 @@
-args: tests/error_006_import_ext_failure.ts --reload
+args: run --reload tests/error_006_import_ext_failure.ts
 check_stderr: true
 exit_code: 1
 output: tests/error_006_import_ext_failure.ts.out
diff --git a/tests/error_007_any.test b/tests/error_007_any.test
index fc0480796..a9f99052a 100644
--- a/tests/error_007_any.test
+++ b/tests/error_007_any.test
@@ -1,4 +1,4 @@
-args: --reload tests/error_007_any.ts
+args: run --reload tests/error_007_any.ts
 check_stderr: true
 exit_code: 1
 output: tests/error_007_any.ts.out
diff --git a/tests/error_008_checkjs.test b/tests/error_008_checkjs.test
index 1944f0bca..ae3a5414a 100644
--- a/tests/error_008_checkjs.test
+++ b/tests/error_008_checkjs.test
@@ -1,4 +1,4 @@
-args: --reload tests/error_008_checkjs.js
+args: run --reload tests/error_008_checkjs.js
 check_stderr: true
 exit_code: 1
 output: tests/error_008_checkjs.js.out
diff --git a/tests/error_syntax.test b/tests/error_syntax.test
index e83cd030f..922226112 100644
--- a/tests/error_syntax.test
+++ b/tests/error_syntax.test
@@ -1,4 +1,4 @@
-args: --reload tests/error_syntax.js
+args: run --reload tests/error_syntax.js
 check_stderr: true
 exit_code: 1
 output: tests/error_syntax.js.out
diff --git a/tests/exit_error42.test b/tests/exit_error42.test
index 21a339a5e..e2c196f6f 100644
--- a/tests/exit_error42.test
+++ b/tests/exit_error42.test
@@ -1,3 +1,3 @@
 exit_code: 42
-args: --reload tests/exit_error42.ts
+args: run --reload tests/exit_error42.ts
 output: tests/exit_error42.ts.out
diff --git a/tests/https_import.test b/tests/https_import.test
index 6cfb53058..1235548da 100644
--- a/tests/https_import.test
+++ b/tests/https_import.test
@@ -1,2 +1,2 @@
-args: --reload tests/https_import.ts
+args: run --reload tests/https_import.ts
 output: tests/https_import.ts.out
diff --git a/tests/if_main.test b/tests/if_main.test
index fe4f061a6..c72c89866 100644
--- a/tests/if_main.test
+++ b/tests/if_main.test
@@ -1,2 +1,2 @@
-args: --reload tests/if_main.ts
+args: run --reload tests/if_main.ts
 output: tests/if_main.ts.out
diff --git a/tests/import_meta.test b/tests/import_meta.test
index bfef5cb56..d38f2d939 100644
--- a/tests/import_meta.test
+++ b/tests/import_meta.test
@@ -1,2 +1,2 @@
-args: --reload tests/import_meta.ts
+args: run --reload tests/import_meta.ts
 output: tests/import_meta.ts.out
diff --git a/tests/unbuffered_stderr.test b/tests/unbuffered_stderr.test
index b3909dc2d..366c1c445 100644
--- a/tests/unbuffered_stderr.test
+++ b/tests/unbuffered_stderr.test
@@ -1,3 +1,3 @@
-args: --reload tests/unbuffered_stderr.ts
+args: run --reload tests/unbuffered_stderr.ts
 check_stderr: true
 output: tests/unbuffered_stderr.ts.out
diff --git a/tests/unbuffered_stdout.test b/tests/unbuffered_stdout.test
index 3ed399cb8..7caa05708 100644
--- a/tests/unbuffered_stdout.test
+++ b/tests/unbuffered_stdout.test
@@ -1,2 +1,2 @@
-args: --reload tests/unbuffered_stdout.ts
+args: run --reload tests/unbuffered_stdout.ts
 output: tests/unbuffered_stdout.ts.out
diff --git a/tests/v8_flags.test b/tests/v8_flags.test
index 66d129bd1..50e00be02 100644
--- a/tests/v8_flags.test
+++ b/tests/v8_flags.test
@@ -1,2 +1,2 @@
-args: --v8-flags=--expose-gc tests/v8_flags.js
+args: run --v8-flags=--expose-gc tests/v8_flags.js
 output: tests/v8_flags.js.out
diff --git a/tests/wasm.test b/tests/wasm.test
index 9e3ecbb28..c4c399670 100644
--- a/tests/wasm.test
+++ b/tests/wasm.test
@@ -1,2 +1,2 @@
-args: tests/wasm.ts
-output: tests/wasm.ts.out
\ No newline at end of file
+args: run tests/wasm.ts
+output: tests/wasm.ts.out
diff --git a/tools/benchmark.py b/tools/benchmark.py
index 55e919643..03fcc497e 100755
--- a/tools/benchmark.py
+++ b/tools/benchmark.py
@@ -143,7 +143,7 @@ def run_strace_benchmarks(deno_exe, new_data):
     thread_count = {}
     syscall_count = {}
     for (name, args) in exec_time_benchmarks:
-        s = get_strace_summary([deno_exe] + args)
+        s = get_strace_summary([deno_exe, "run"] + args)
         thread_count[name] = s["clone"]["calls"] + 1
         syscall_count[name] = s["total"]["calls"]
     new_data["thread_count"] = thread_count
@@ -162,7 +162,7 @@ def find_max_mem_in_bytes(time_v_output):
 def run_max_mem_benchmark(deno_exe):
     results = {}
     for (name, args) in exec_time_benchmarks:
-        cmd = ["/usr/bin/time", "-v", deno_exe] + args
+        cmd = ["/usr/bin/time", "-v", deno_exe, "run"] + args
         try:
             out = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
         except subprocess.CalledProcessError:
@@ -179,7 +179,8 @@ def run_exec_time(deno_exe, build_dir):
         hyperfine, "--ignore-failure", "--export-json", benchmark_file,
         "--warmup", "3"
     ] + [
-        deno_exe + " " + " ".join(args) for [_, args] in exec_time_benchmarks
+        deno_exe + " run " + " ".join(args)
+        for [_, args] in exec_time_benchmarks
     ])
     hyperfine_results = read_json(benchmark_file)
     results = {}
diff --git a/tools/deno_dir_test.py b/tools/deno_dir_test.py
index 4b6c3d8aa..bcfa370bf 100755
--- a/tools/deno_dir_test.py
+++ b/tools/deno_dir_test.py
@@ -35,7 +35,7 @@ def deno_dir_test(deno_exe, deno_dir):
 
 
 def run_deno(deno_exe, deno_dir=None):
-    cmd = [deno_exe, "tests/002_hello.ts"]
+    cmd = [deno_exe, "run", "tests/002_hello.ts"]
     deno_dir_env = {"DENO_DIR": deno_dir} if deno_dir is not None else None
     run(cmd, quiet=True, env=deno_dir_env)
 
diff --git a/tools/http_benchmark.py b/tools/http_benchmark.py
index 7db900a86..68d68e44a 100755
--- a/tools/http_benchmark.py
+++ b/tools/http_benchmark.py
@@ -11,14 +11,14 @@ DURATION = "10s"
 
 
 def deno_http_benchmark(deno_exe):
-    deno_cmd = [deno_exe, "--allow-net", "tests/http_bench.ts", ADDR]
+    deno_cmd = [deno_exe, "run", "--allow-net", "tests/http_bench.ts", ADDR]
     print "http_benchmark testing DENO."
     return run(deno_cmd)
 
 
 def deno_net_http_benchmark(deno_exe):
     deno_cmd = [
-        deno_exe, "--allow-net",
+        deno_exe, "run", "--allow-net",
         "js/deps/https/deno.land/std/http/http_bench.ts", ADDR
     ]
     print "http_benchmark testing DENO using net/http."
diff --git a/tools/is_tty_test.py b/tools/is_tty_test.py
index 867fd7a1c..6f7509a8c 100755
--- a/tools/is_tty_test.py
+++ b/tools/is_tty_test.py
@@ -12,7 +12,7 @@ IS_TTY_TEST_TS = "tests/is_tty.ts"
 
 
 def is_tty_test(deno_exe):
-    cmd = [deno_exe, IS_TTY_TEST_TS]
+    cmd = [deno_exe, "run", IS_TTY_TEST_TS]
     code, stdout, _ = tty_capture(cmd, b'')
     assert code == 0
     assert str(stdin.isatty()).lower() in stdout
diff --git a/tools/permission_prompt_test.py b/tools/permission_prompt_test.py
index 6e8922640..e3ee7d9c8 100755
--- a/tools/permission_prompt_test.py
+++ b/tools/permission_prompt_test.py
@@ -71,7 +71,8 @@ class Prompt(object):
 
     def run(self, flags, args, bytes_input):
         "Returns (return_code, stdout, stderr)."
-        cmd = [self.deno_exe] + flags + [PERMISSIONS_PROMPT_TEST_TS] + args
+        cmd = [self.deno_exe, "run"] + flags + [PERMISSIONS_PROMPT_TEST_TS
+                                                ] + args
         return tty_capture(cmd, bytes_input)
 
     def warm_up(self):
diff --git a/tools/repl_test.py b/tools/repl_test.py
index 59346d3e8..9ea1b82af 100644
--- a/tools/repl_test.py
+++ b/tools/repl_test.py
@@ -19,7 +19,7 @@ class Repl(object):
     def input(self, *lines, **kwargs):
         exit_ = kwargs.pop("exit", True)
         sleep_ = kwargs.pop("sleep", 0)
-        p = Popen([self.deno_exe, "-A"], stdout=PIPE, stderr=PIPE, stdin=PIPE)
+        p = Popen([self.deno_exe], stdout=PIPE, stderr=PIPE, stdin=PIPE)
         try:
             # Note: The repl takes a >100ms until it's ready.
             time.sleep(sleep_)
diff --git a/tools/test.py b/tools/test.py
index e4914ae50..2a59a0c87 100755
--- a/tools/test.py
+++ b/tools/test.py
@@ -30,16 +30,16 @@ def test_no_color(deno_exe):
     sys.stdout.write("no_color test...")
     sys.stdout.flush()
     t = os.path.join(tests_path, "no_color.js")
-    output = run_output([deno_exe, t], merge_env={"NO_COLOR": "1"})
+    output = run_output([deno_exe, "run", t], merge_env={"NO_COLOR": "1"})
     assert output.strip() == "noColor true"
     t = os.path.join(tests_path, "no_color.js")
-    output = run_output([deno_exe, t])
+    output = run_output([deno_exe, "run", t])
     assert output.strip() == "noColor false"
     print green_ok()
 
 
 def exec_path_test(deno_exe):
-    cmd = [deno_exe, "tests/exec_path.ts"]
+    cmd = [deno_exe, "run", "tests/exec_path.ts"]
     output = run_output(cmd)
     assert deno_exe in output.strip()
 
diff --git a/tools/throughput_benchmark.py b/tools/throughput_benchmark.py
index 712edfe43..9343d9613 100755
--- a/tools/throughput_benchmark.py
+++ b/tools/throughput_benchmark.py
@@ -19,7 +19,8 @@ ADDR = "127.0.0.1:4544"
 def cat(deno_exe, megs):
     size = megs * MB
     start = time.time()
-    cmd = deno_exe + " --allow-read tests/cat.ts /dev/zero | head -c %s " % size
+    cmd = deno_exe + " run --allow-read "
+    cmd += "tests/cat.ts /dev/zero | head -c %s " % size
     print cmd
     subprocess.check_output(cmd, shell=True)
     end = time.time()
@@ -30,7 +31,7 @@ def tcp(deno_exe, megs):
     size = megs * MB
     # Run deno echo server in the background.
     echo_server = subprocess.Popen(
-        [deno_exe, "--allow-net", "tests/echo_server.ts", ADDR])
+        [deno_exe, "run", "--allow-net", "tests/echo_server.ts", ADDR])
 
     time.sleep(5)  # wait for deno to wake up. TODO racy.
     try:
diff --git a/tools/unit_tests.py b/tools/unit_tests.py
index abc9baf06..14284b325 100755
--- a/tools/unit_tests.py
+++ b/tools/unit_tests.py
@@ -34,7 +34,7 @@ def run_unit_test2(cmd):
 def run_unit_test(deno_exe, permStr, flags=None):
     if flags is None:
         flags = []
-    cmd = [deno_exe] + flags + ["js/unit_tests.ts", permStr]
+    cmd = [deno_exe, "run"] + flags + ["js/unit_tests.ts", permStr]
     run_unit_test2(cmd)
 
 
diff --git a/website/index.html b/website/index.html
index f1cbde49f..4af6d67a4 100644
--- a/website/index.html
+++ b/website/index.html
@@ -104,7 +104,7 @@ href="https://github.com/denoland/deno_install/blob/master/install.ps1">https://
       <h2 id="example">Example <a href="#example">#</a></h2>
 
       <p>Try running a simple program:</p>
-      <pre>deno https://deno.land/welcome.ts</pre>
+      <pre>deno run https://deno.land/welcome.ts</pre>
 
       <p>Or a more complex one:</p>
 
diff --git a/website/manual.md b/website/manual.md
index bfc8f9603..efa867b18 100644
--- a/website/manual.md
+++ b/website/manual.md
@@ -543,31 +543,24 @@ USAGE:
     deno [FLAGS] [OPTIONS] [SUBCOMMAND]
 
 FLAGS:
-    -A, --allow-all               Allow all permissions
-        --allow-env               Allow environment access
-        --allow-high-precision    Allow high precision time measurement
-        --allow-net               Allow network access
-        --allow-read              Allow file system read access
-        --allow-run               Allow running subprocesses
-        --allow-write             Allow file system write access
-    -h, --help                    Prints help information
-    -D, --log-debug               Log debug output
-        --no-prompt               Do not use prompts
-    -r, --reload                  Reload source code cache (recompile TypeScript)
-        --v8-options              Print V8 command line options
+    -h, --help          Prints help information
+    -D, --log-debug     Log debug output
+    -r, --reload        Reload source code cache (recompile TypeScript)
+        --v8-options    Print V8 command line options
 
 OPTIONS:
+    -c, --config <FILE>          Load compiler configuration file
         --v8-flags=<v8-flags>    Set V8 command line options
 
 SUBCOMMANDS:
-    <script>    Script to run
-    eval        Eval script
-    fetch       Fetch the dependencies
-    fmt         Format files
-    help        Prints this message or the help of the given subcommand(s)
-    info        Show source file related info
-    types       Print runtime TypeScript declarations
-    version     Print the version
+    eval       Eval script
+    fetch      Fetch the dependencies
+    fmt        Format files
+    help       Prints this message or the help of the given subcommand(s)
+    info       Show source file related info
+    run        Run a program given a filename or url to the source code
+    types      Print runtime TypeScript declarations
+    version    Print the version
 
 ENVIRONMENT VARIABLES:
     DENO_DIR        Set deno's base directory