diff --git a/cli/config_file.rs b/cli/args/config_file.rs
similarity index 99%
rename from cli/config_file.rs
rename to cli/args/config_file.rs
index 4b2596ba2d..bed155d324 100644
--- a/cli/config_file.rs
+++ b/cli/args/config_file.rs
@@ -1,7 +1,7 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
-use crate::flags::ConfigFlag;
-use crate::flags::Flags;
+use crate::args::ConfigFlag;
+use crate::args::Flags;
 use crate::fs_util::canonicalize_path;
 use crate::fs_util::specifier_parent;
 use crate::fs_util::specifier_to_file_path;
diff --git a/cli/flags.rs b/cli/args/flags.rs
similarity index 99%
rename from cli/flags.rs
rename to cli/args/flags.rs
index 383d78a995..c61e9ab210 100644
--- a/cli/flags.rs
+++ b/cli/args/flags.rs
@@ -20,6 +20,8 @@ use std::num::NonZeroUsize;
 use std::path::PathBuf;
 use std::str::FromStr;
 
+use super::flags_allow_net;
+
 static LONG_VERSION: Lazy<String> = Lazy::new(|| {
   format!(
     "{} ({}, {})\nv8 {}\ntypescript {}",
@@ -1746,7 +1748,7 @@ fn permission_args(app: Command) -> Command {
         .use_value_delimiter(true)
         .require_equals(true)
         .help("Allow network access")
-        .validator(crate::flags_allow_net::validator),
+        .validator(flags_allow_net::validator),
     )
     .arg(unsafely_ignore_certificate_errors_arg())
     .arg(
@@ -2126,7 +2128,7 @@ fn unsafely_ignore_certificate_errors_arg<'a>() -> Arg<'a> {
     .require_equals(true)
     .value_name("HOSTNAMES")
     .help("DANGER: Disables verification of TLS certificates")
-    .validator(crate::flags_allow_net::validator)
+    .validator(flags_allow_net::validator)
 }
 
 fn bench_parse(flags: &mut Flags, matches: &clap::ArgMatches) {
@@ -2773,7 +2775,7 @@ fn permission_args_parse(flags: &mut Flags, matches: &clap::ArgMatches) {
 
   if let Some(net_wl) = matches.values_of("allow-net") {
     let net_allowlist: Vec<String> =
-      crate::flags_allow_net::parse(net_wl.map(ToString::to_string).collect())
+      flags_allow_net::parse(net_wl.map(ToString::to_string).collect())
         .unwrap();
     flags.allow_net = Some(net_allowlist);
   }
@@ -2831,8 +2833,7 @@ fn unsafely_ignore_certificate_errors_parse(
 ) {
   if let Some(ic_wl) = matches.values_of("unsafely-ignore-certificate-errors") {
     let ic_allowlist: Vec<String> =
-      crate::flags_allow_net::parse(ic_wl.map(ToString::to_string).collect())
-        .unwrap();
+      flags_allow_net::parse(ic_wl.map(ToString::to_string).collect()).unwrap();
     flags.unsafely_ignore_certificate_errors = Some(ic_allowlist);
   }
 }
diff --git a/cli/flags_allow_net.rs b/cli/args/flags_allow_net.rs
similarity index 100%
rename from cli/flags_allow_net.rs
rename to cli/args/flags_allow_net.rs
diff --git a/cli/args/mod.rs b/cli/args/mod.rs
new file mode 100644
index 0000000000..375a531221
--- /dev/null
+++ b/cli/args/mod.rs
@@ -0,0 +1,9 @@
+// Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
+
+pub mod config_file;
+pub mod flags;
+
+mod flags_allow_net;
+
+pub use config_file::*;
+pub use flags::*;
diff --git a/cli/emit.rs b/cli/emit.rs
index 10089bc8a2..8246e17209 100644
--- a/cli/emit.rs
+++ b/cli/emit.rs
@@ -4,15 +4,15 @@
 //! populate a cache, emit files, and transform a graph into the structures for
 //! loading into an isolate.
 
+use crate::args::ConfigFile;
+use crate::args::EmitConfigOptions;
+use crate::args::IgnoredCompilerOptions;
+use crate::args::TsConfig;
+use crate::args::TypeCheckMode;
 use crate::cache::CacheType;
 use crate::cache::Cacher;
 use crate::colors;
-use crate::config_file;
-use crate::config_file::ConfigFile;
-use crate::config_file::IgnoredCompilerOptions;
-use crate::config_file::TsConfig;
 use crate::diagnostics::Diagnostics;
-use crate::flags;
 use crate::graph_util::GraphData;
 use crate::graph_util::ModuleEntry;
 use crate::tsc;
@@ -372,7 +372,7 @@ pub fn is_emittable(
 pub struct CheckOptions {
   /// The check flag from the option which can effect the filtering of
   /// diagnostics in the emit result.
-  pub type_check_mode: flags::TypeCheckMode,
+  pub type_check_mode: TypeCheckMode,
   /// Set the debug flag on the TypeScript type checker.
   pub debug: bool,
   /// If true, any files emitted will be cached, even if there are diagnostics
@@ -463,7 +463,7 @@ pub fn check_and_maybe_emit(
     root_names,
   })?;
 
-  let diagnostics = if options.type_check_mode == flags::TypeCheckMode::Local {
+  let diagnostics = if options.type_check_mode == TypeCheckMode::Local {
     response.diagnostics.filter(|d| {
       if let Some(file_name) = &d.file_name {
         !file_name.starts_with("http")
@@ -772,10 +772,9 @@ impl Hook for BundleHook {
   }
 }
 
-impl From<config_file::TsConfig> for deno_ast::EmitOptions {
-  fn from(config: config_file::TsConfig) -> Self {
-    let options: config_file::EmitConfigOptions =
-      serde_json::from_value(config.0).unwrap();
+impl From<TsConfig> for deno_ast::EmitOptions {
+  fn from(config: TsConfig) -> Self {
+    let options: EmitConfigOptions = serde_json::from_value(config.0).unwrap();
     let imports_not_used_as_values =
       match options.imports_not_used_as_values.as_str() {
         "preserve" => deno_ast::ImportsNotUsedAsValues::Preserve,
diff --git a/cli/lsp/analysis.rs b/cli/lsp/analysis.rs
index 8e9b4ccaaa..2508862833 100644
--- a/cli/lsp/analysis.rs
+++ b/cli/lsp/analysis.rs
@@ -5,7 +5,7 @@ use super::documents::Documents;
 use super::language_server;
 use super::tsc;
 
-use crate::config_file::LintConfig;
+use crate::args::LintConfig;
 use crate::tools::lint::create_linter;
 use crate::tools::lint::get_configured_rules;
 
diff --git a/cli/lsp/cache.rs b/cli/lsp/cache.rs
index 249177a64e..0f76082789 100644
--- a/cli/lsp/cache.rs
+++ b/cli/lsp/cache.rs
@@ -1,8 +1,8 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::ConfigFile;
+use crate::args::Flags;
 use crate::cache::FetchCacher;
-use crate::config_file::ConfigFile;
-use crate::flags::Flags;
 use crate::graph_util::graph_valid;
 use crate::http_cache;
 use crate::proc_state::ProcState;
diff --git a/cli/lsp/diagnostics.rs b/cli/lsp/diagnostics.rs
index fe3b5ee453..52ba1ba969 100644
--- a/cli/lsp/diagnostics.rs
+++ b/cli/lsp/diagnostics.rs
@@ -13,7 +13,7 @@ use super::performance::Performance;
 use super::tsc;
 use super::tsc::TsServer;
 
-use crate::config_file::LintConfig;
+use crate::args::LintConfig;
 use crate::diagnostics;
 
 use deno_ast::MediaType;
diff --git a/cli/lsp/documents.rs b/cli/lsp/documents.rs
index ec1e183aea..4cc0beb2a3 100644
--- a/cli/lsp/documents.rs
+++ b/cli/lsp/documents.rs
@@ -5,7 +5,7 @@ use super::text::LineIndex;
 use super::tsc;
 use super::tsc::AssetDocument;
 
-use crate::config_file::ConfigFile;
+use crate::args::ConfigFile;
 use crate::file_fetcher::get_source_from_bytes;
 use crate::file_fetcher::map_content_type;
 use crate::file_fetcher::SUPPORTED_SCHEMES;
diff --git a/cli/lsp/language_server.rs b/cli/lsp/language_server.rs
index 30a2ce2533..4a703c7192 100644
--- a/cli/lsp/language_server.rs
+++ b/cli/lsp/language_server.rs
@@ -54,10 +54,10 @@ use super::tsc::Assets;
 use super::tsc::AssetsSnapshot;
 use super::tsc::TsServer;
 use super::urls;
-use crate::config_file::ConfigFile;
-use crate::config_file::FmtConfig;
-use crate::config_file::LintConfig;
-use crate::config_file::TsConfig;
+use crate::args::ConfigFile;
+use crate::args::FmtConfig;
+use crate::args::LintConfig;
+use crate::args::TsConfig;
 use crate::deno_dir;
 use crate::file_fetcher::get_source_from_data_url;
 use crate::fs_util;
@@ -364,8 +364,7 @@ impl Inner {
     if let Some(root_uri) = &self.config.root_uri {
       let root_path = fs_util::specifier_to_file_path(root_uri)?;
       let mut checked = std::collections::HashSet::new();
-      let maybe_config =
-        crate::config_file::discover_from(&root_path, &mut checked)?;
+      let maybe_config = crate::args::discover_from(&root_path, &mut checked)?;
       Ok(maybe_config.map(|c| {
         lsp_log!("  Auto-resolved configuration file: \"{}\"", c.specifier);
         c
diff --git a/cli/lsp/testing/execution.rs b/cli/lsp/testing/execution.rs
index 03fdba63c4..6b4e947a0a 100644
--- a/cli/lsp/testing/execution.rs
+++ b/cli/lsp/testing/execution.rs
@@ -4,10 +4,11 @@ use super::definitions::TestDefinition;
 use super::definitions::TestDefinitions;
 use super::lsp_custom;
 
+use crate::args::flags_from_vec;
+use crate::args::DenoSubcommand;
 use crate::checksum;
 use crate::create_main_worker;
 use crate::emit;
-use crate::flags;
 use crate::located_script_name;
 use crate::lsp::client::Client;
 use crate::lsp::client::TestingNotification;
@@ -306,8 +307,7 @@ impl TestRun {
   ) -> Result<(), AnyError> {
     let args = self.get_args();
     lsp_log!("Executing test run with arguments: {}", args.join(" "));
-    let flags =
-      flags::flags_from_vec(args.into_iter().map(String::from).collect())?;
+    let flags = flags_from_vec(args.into_iter().map(String::from).collect())?;
     let ps = proc_state::ProcState::build(Arc::new(flags)).await?;
     let permissions =
       Permissions::from_options(&ps.flags.permissions_options());
@@ -327,7 +327,7 @@ impl TestRun {
     let sender = TestEventSender::new(sender);
 
     let (concurrent_jobs, fail_fast) =
-      if let flags::DenoSubcommand::Test(test_flags) = &ps.flags.subcommand {
+      if let DenoSubcommand::Test(test_flags) = &ps.flags.subcommand {
         (
           test_flags.concurrent_jobs.into(),
           test_flags.fail_fast.map(|count| count.into()),
diff --git a/cli/lsp/tsc.rs b/cli/lsp/tsc.rs
index 76e428b2f2..9988a0ac9e 100644
--- a/cli/lsp/tsc.rs
+++ b/cli/lsp/tsc.rs
@@ -17,7 +17,7 @@ use super::text::LineIndex;
 use super::urls::LspUrlMap;
 use super::urls::INVALID_SPECIFIER;
 
-use crate::config_file::TsConfig;
+use crate::args::TsConfig;
 use crate::fs_util::specifier_to_file_path;
 use crate::tsc;
 use crate::tsc::ResolveArgs;
diff --git a/cli/main.rs b/cli/main.rs
index d9c4486f4a..e74ed8518b 100644
--- a/cli/main.rs
+++ b/cli/main.rs
@@ -1,11 +1,11 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+mod args;
 mod auth_tokens;
 mod cache;
 mod cdp;
 mod checksum;
 mod compat;
-mod config_file;
 mod deno_dir;
 mod diagnostics;
 mod diff;
@@ -15,8 +15,6 @@ mod emit;
 mod errors;
 mod file_fetcher;
 mod file_watcher;
-mod flags;
-mod flags_allow_net;
 mod fmt_errors;
 mod fs_util;
 mod graph_util;
@@ -37,31 +35,33 @@ mod unix_util;
 mod version;
 mod windows_util;
 
+use crate::args::flags_from_vec;
+use crate::args::resolve_import_map_specifier;
+use crate::args::BenchFlags;
+use crate::args::BundleFlags;
+use crate::args::CacheFlags;
+use crate::args::CheckFlags;
+use crate::args::CompileFlags;
+use crate::args::CompletionsFlags;
+use crate::args::CoverageFlags;
+use crate::args::DenoSubcommand;
+use crate::args::DocFlags;
+use crate::args::EvalFlags;
+use crate::args::Flags;
+use crate::args::FmtFlags;
+use crate::args::InfoFlags;
+use crate::args::InstallFlags;
+use crate::args::LintFlags;
+use crate::args::ReplFlags;
+use crate::args::RunFlags;
+use crate::args::TaskFlags;
+use crate::args::TestFlags;
+use crate::args::TypeCheckMode;
+use crate::args::UninstallFlags;
+use crate::args::UpgradeFlags;
+use crate::args::VendorFlags;
 use crate::file_fetcher::File;
 use crate::file_watcher::ResolutionResult;
-use crate::flags::BenchFlags;
-use crate::flags::BundleFlags;
-use crate::flags::CacheFlags;
-use crate::flags::CheckFlags;
-use crate::flags::CompileFlags;
-use crate::flags::CompletionsFlags;
-use crate::flags::CoverageFlags;
-use crate::flags::DenoSubcommand;
-use crate::flags::DocFlags;
-use crate::flags::EvalFlags;
-use crate::flags::Flags;
-use crate::flags::FmtFlags;
-use crate::flags::InfoFlags;
-use crate::flags::InstallFlags;
-use crate::flags::LintFlags;
-use crate::flags::ReplFlags;
-use crate::flags::RunFlags;
-use crate::flags::TaskFlags;
-use crate::flags::TestFlags;
-use crate::flags::TypeCheckMode;
-use crate::flags::UninstallFlags;
-use crate::flags::UpgradeFlags;
-use crate::flags::VendorFlags;
 use crate::fmt_errors::format_js_error;
 use crate::graph_util::graph_lock_or_exit;
 use crate::graph_util::graph_valid;
@@ -69,6 +69,7 @@ use crate::module_loader::CliModuleLoader;
 use crate::proc_state::ProcState;
 use crate::resolver::ImportMapResolver;
 use crate::resolver::JsxResolver;
+
 use deno_ast::MediaType;
 use deno_core::error::generic_error;
 use deno_core::error::AnyError;
@@ -797,12 +798,11 @@ async fn bundle_command(
         })
         .collect();
 
-      if let Ok(Some(import_map_path)) =
-        config_file::resolve_import_map_specifier(
-          ps.flags.import_map_path.as_deref(),
-          ps.maybe_config_file.as_ref(),
-        )
-        .map(|ms| ms.and_then(|ref s| s.to_file_path().ok()))
+      if let Ok(Some(import_map_path)) = resolve_import_map_specifier(
+        ps.flags.import_map_path.as_deref(),
+        ps.maybe_config_file.as_ref(),
+      )
+      .map(|ms| ms.and_then(|ref s| s.to_file_path().ok()))
       {
         paths_to_watch.push(import_map_path);
       }
@@ -1418,7 +1418,7 @@ pub fn main() {
     // TODO(bartlomieju): doesn't handle exit code set by the runtime properly
     unwrap_or_exit(standalone_res);
 
-    let flags = match flags::flags_from_vec(args) {
+    let flags = match flags_from_vec(args) {
       Ok(flags) => flags,
       Err(err @ clap::Error { .. })
         if err.kind() == clap::ErrorKind::DisplayHelp
diff --git a/cli/proc_state.rs b/cli/proc_state.rs
index e06c3f7725..112307eb40 100644
--- a/cli/proc_state.rs
+++ b/cli/proc_state.rs
@@ -1,19 +1,20 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::resolve_import_map_specifier;
+use crate::args::ConfigFile;
+use crate::args::Flags;
+use crate::args::MaybeImportsResult;
+use crate::args::TypeCheckMode;
 use crate::cache;
 use crate::colors;
 use crate::compat;
 use crate::compat::NodeEsmResolver;
-use crate::config_file;
-use crate::config_file::ConfigFile;
-use crate::config_file::MaybeImportsResult;
 use crate::deno_dir;
 use crate::emit;
 use crate::emit::EmitCache;
 use crate::file_fetcher::get_root_cert_store;
 use crate::file_fetcher::CacheSetting;
 use crate::file_fetcher::FileFetcher;
-use crate::flags;
 use crate::graph_util::graph_lock_or_exit;
 use crate::graph_util::GraphData;
 use crate::graph_util::ModuleEntry;
@@ -68,7 +69,7 @@ pub struct ProcState(Arc<Inner>);
 
 pub struct Inner {
   /// Flags parsed from `argv` contents.
-  pub flags: Arc<flags::Flags>,
+  pub flags: Arc<Flags>,
   pub dir: deno_dir::DenoDir,
   pub coverage_dir: Option<String>,
   pub file_fetcher: FileFetcher,
@@ -94,12 +95,12 @@ impl Deref for ProcState {
 }
 
 impl ProcState {
-  pub async fn build(flags: Arc<flags::Flags>) -> Result<Self, AnyError> {
+  pub async fn build(flags: Arc<Flags>) -> Result<Self, AnyError> {
     Self::build_with_sender(flags, None).await
   }
 
   pub async fn build_for_file_watcher(
-    flags: Arc<flags::Flags>,
+    flags: Arc<Flags>,
     files_to_watch_sender: tokio::sync::mpsc::UnboundedSender<Vec<PathBuf>>,
   ) -> Result<Self, AnyError> {
     let ps = Self::build_with_sender(
@@ -113,12 +114,11 @@ impl ProcState {
       files_to_watch_sender.send(watch_paths.clone()).unwrap();
     }
 
-    if let Ok(Some(import_map_path)) =
-      config_file::resolve_import_map_specifier(
-        ps.flags.import_map_path.as_deref(),
-        ps.maybe_config_file.as_ref(),
-      )
-      .map(|ms| ms.and_then(|ref s| s.to_file_path().ok()))
+    if let Ok(Some(import_map_path)) = resolve_import_map_specifier(
+      ps.flags.import_map_path.as_deref(),
+      ps.maybe_config_file.as_ref(),
+    )
+    .map(|ms| ms.and_then(|ref s| s.to_file_path().ok()))
     {
       files_to_watch_sender.send(vec![import_map_path]).unwrap();
     }
@@ -127,7 +127,7 @@ impl ProcState {
   }
 
   async fn build_with_sender(
-    flags: Arc<flags::Flags>,
+    flags: Arc<Flags>,
     maybe_sender: Option<tokio::sync::mpsc::UnboundedSender<Vec<PathBuf>>>,
   ) -> Result<Self, AnyError> {
     let maybe_custom_root = flags
@@ -188,13 +188,12 @@ impl ProcState {
       None
     };
 
-    let maybe_config_file = crate::config_file::discover(&flags)?;
+    let maybe_config_file = crate::args::discover(&flags)?;
 
-    let maybe_import_map_specifier =
-      crate::config_file::resolve_import_map_specifier(
-        flags.import_map_path.as_deref(),
-        maybe_config_file.as_ref(),
-      )?;
+    let maybe_import_map_specifier = crate::args::resolve_import_map_specifier(
+      flags.import_map_path.as_deref(),
+      maybe_config_file.as_ref(),
+    )?;
 
     let maybe_import_map =
       if let Some(import_map_specifier) = maybe_import_map_specifier {
@@ -349,12 +348,12 @@ impl ProcState {
     };
     if !reload_on_watch {
       let graph_data = self.graph_data.read();
-      if self.flags.type_check_mode == flags::TypeCheckMode::None
+      if self.flags.type_check_mode == TypeCheckMode::None
         || graph_data.is_type_checked(&roots, &lib)
       {
         if let Some(result) = graph_data.check(
           &roots,
-          self.flags.type_check_mode != flags::TypeCheckMode::None,
+          self.flags.type_check_mode != TypeCheckMode::None,
           false,
         ) {
           return result;
@@ -471,21 +470,20 @@ impl ProcState {
       graph_data
         .check(
           &roots,
-          self.flags.type_check_mode != flags::TypeCheckMode::None,
+          self.flags.type_check_mode != TypeCheckMode::None,
           check_js,
         )
         .unwrap()?;
     }
 
-    let config_type =
-      if self.flags.type_check_mode == flags::TypeCheckMode::None {
-        emit::ConfigType::Emit
-      } else {
-        emit::ConfigType::Check {
-          tsc_emit: true,
-          lib: lib.clone(),
-        }
-      };
+    let config_type = if self.flags.type_check_mode == TypeCheckMode::None {
+      emit::ConfigType::Emit
+    } else {
+      emit::ConfigType::Check {
+        tsc_emit: true,
+        lib: lib.clone(),
+      }
+    };
 
     let (ts_config, maybe_ignored_options) =
       emit::get_ts_config(config_type, self.maybe_config_file.as_ref(), None)?;
@@ -494,7 +492,7 @@ impl ProcState {
       log::warn!("{}", ignored_options);
     }
 
-    if self.flags.type_check_mode == flags::TypeCheckMode::None {
+    if self.flags.type_check_mode == TypeCheckMode::None {
       let options = emit::EmitOptions {
         ts_config,
         reload: self.flags.reload,
@@ -529,7 +527,7 @@ impl ProcState {
       log::debug!("{}", emit_result.stats);
     }
 
-    if self.flags.type_check_mode != flags::TypeCheckMode::None {
+    if self.flags.type_check_mode != TypeCheckMode::None {
       let mut graph_data = self.graph_data.write();
       graph_data.set_type_checked(&roots, &lib);
     }
diff --git a/cli/standalone.rs b/cli/standalone.rs
index 1e8429db04..d66eb7694a 100644
--- a/cli/standalone.rs
+++ b/cli/standalone.rs
@@ -1,8 +1,8 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::Flags;
 use crate::colors;
 use crate::file_fetcher::get_source_from_data_url;
-use crate::flags::Flags;
 use crate::fmt_errors::format_js_error;
 use crate::ops;
 use crate::proc_state::ProcState;
diff --git a/cli/tools/bench.rs b/cli/tools/bench.rs
index b51938d133..3c40b4e951 100644
--- a/cli/tools/bench.rs
+++ b/cli/tools/bench.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::BenchFlags;
+use crate::args::Flags;
+use crate::args::TypeCheckMode;
 use crate::cache;
 use crate::colors;
 use crate::compat;
@@ -7,9 +10,6 @@ use crate::create_main_worker;
 use crate::emit;
 use crate::file_watcher;
 use crate::file_watcher::ResolutionResult;
-use crate::flags::BenchFlags;
-use crate::flags::Flags;
-use crate::flags::TypeCheckMode;
 use crate::fs_util::collect_specifiers;
 use crate::fs_util::is_supported_bench_path;
 use crate::graph_util::contains_specifier;
diff --git a/cli/tools/coverage/mod.rs b/cli/tools/coverage/mod.rs
index d895f8a7e7..efaf199220 100644
--- a/cli/tools/coverage/mod.rs
+++ b/cli/tools/coverage/mod.rs
@@ -1,8 +1,8 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::CoverageFlags;
+use crate::args::Flags;
 use crate::colors;
-use crate::flags::CoverageFlags;
-use crate::flags::Flags;
 use crate::fs_util::collect_files;
 use crate::proc_state::ProcState;
 use crate::tools::fmt::format_json;
diff --git a/cli/tools/doc.rs b/cli/tools/doc.rs
index a5826d1bc0..684c3040e4 100644
--- a/cli/tools/doc.rs
+++ b/cli/tools/doc.rs
@@ -1,9 +1,9 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::DocFlags;
+use crate::args::Flags;
 use crate::colors;
 use crate::file_fetcher::File;
-use crate::flags::DocFlags;
-use crate::flags::Flags;
 use crate::get_types;
 use crate::proc_state::ProcState;
 use crate::write_json_to_stdout;
diff --git a/cli/tools/fmt.rs b/cli/tools/fmt.rs
index 7758f29f9c..b2aa473737 100644
--- a/cli/tools/fmt.rs
+++ b/cli/tools/fmt.rs
@@ -7,16 +7,16 @@
 //! the future it can be easily extended to provide
 //! the same functions as ops available in JS runtime.
 
+use crate::args::Flags;
+use crate::args::FmtConfig;
+use crate::args::FmtFlags;
+use crate::args::FmtOptionsConfig;
+use crate::args::ProseWrap;
 use crate::colors;
-use crate::config_file::FmtConfig;
-use crate::config_file::FmtOptionsConfig;
-use crate::config_file::ProseWrap;
 use crate::deno_dir::DenoDir;
 use crate::diff::diff;
 use crate::file_watcher;
 use crate::file_watcher::ResolutionResult;
-use crate::flags::Flags;
-use crate::flags::FmtFlags;
 use crate::fs_util::collect_files;
 use crate::fs_util::get_extension;
 use crate::fs_util::specifier_to_file_path;
diff --git a/cli/tools/installer.rs b/cli/tools/installer.rs
index 962f16ce37..df4b463322 100644
--- a/cli/tools/installer.rs
+++ b/cli/tools/installer.rs
@@ -1,9 +1,9 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
-use crate::flags::ConfigFlag;
-use crate::flags::Flags;
-use crate::flags::InstallFlags;
-use crate::flags::TypeCheckMode;
+use crate::args::ConfigFlag;
+use crate::args::Flags;
+use crate::args::InstallFlags;
+use crate::args::TypeCheckMode;
 use crate::fs_util::canonicalize_path;
 use deno_core::error::generic_error;
 use deno_core::error::AnyError;
@@ -403,7 +403,7 @@ fn is_in_path(dir: &Path) -> bool {
 mod tests {
   use super::*;
 
-  use crate::flags::ConfigFlag;
+  use crate::args::ConfigFlag;
   use std::process::Command;
   use test_util::testdata_path;
   use test_util::TempDir;
diff --git a/cli/tools/lint.rs b/cli/tools/lint.rs
index f251dc6475..60cda9f906 100644
--- a/cli/tools/lint.rs
+++ b/cli/tools/lint.rs
@@ -6,9 +6,9 @@
 //! At the moment it is only consumed using CLI but in
 //! the future it can be easily extended to provide
 //! the same functions as ops available in JS runtime.
-use crate::config_file::LintConfig;
+use crate::args::LintConfig;
+use crate::args::{Flags, LintFlags};
 use crate::file_watcher::ResolutionResult;
-use crate::flags::{Flags, LintFlags};
 use crate::fmt_errors;
 use crate::fs_util::{collect_files, is_supported_ext, specifier_to_file_path};
 use crate::proc_state::ProcState;
@@ -590,7 +590,7 @@ mod test {
   use deno_lint::rules::get_recommended_rules;
 
   use super::*;
-  use crate::config_file::LintRulesConfig;
+  use crate::args::LintRulesConfig;
 
   #[test]
   fn recommended_rules_when_no_tags_in_config() {
diff --git a/cli/tools/standalone.rs b/cli/tools/standalone.rs
index e29545b2ff..2561188ca7 100644
--- a/cli/tools/standalone.rs
+++ b/cli/tools/standalone.rs
@@ -1,11 +1,11 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::CompileFlags;
+use crate::args::DenoSubcommand;
+use crate::args::Flags;
+use crate::args::RunFlags;
+use crate::args::TypeCheckMode;
 use crate::deno_dir::DenoDir;
-use crate::flags::CompileFlags;
-use crate::flags::DenoSubcommand;
-use crate::flags::Flags;
-use crate::flags::RunFlags;
-use crate::flags::TypeCheckMode;
 use crate::fs_util;
 use crate::standalone::Metadata;
 use crate::standalone::MAGIC_TRAILER;
diff --git a/cli/tools/task.rs b/cli/tools/task.rs
index 28dd0a8536..1b6846e7ce 100644
--- a/cli/tools/task.rs
+++ b/cli/tools/task.rs
@@ -1,9 +1,9 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::ConfigFile;
+use crate::args::Flags;
+use crate::args::TaskFlags;
 use crate::colors;
-use crate::config_file::ConfigFile;
-use crate::flags::Flags;
-use crate::flags::TaskFlags;
 use crate::fs_util;
 use crate::proc_state::ProcState;
 use deno_core::anyhow::bail;
diff --git a/cli/tools/test.rs b/cli/tools/test.rs
index 94412a3ae8..ac146fdbf7 100644
--- a/cli/tools/test.rs
+++ b/cli/tools/test.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::Flags;
+use crate::args::TestFlags;
+use crate::args::TypeCheckMode;
 use crate::cache;
 use crate::colors;
 use crate::compat;
@@ -9,9 +12,6 @@ use crate::emit;
 use crate::file_fetcher::File;
 use crate::file_watcher;
 use crate::file_watcher::ResolutionResult;
-use crate::flags::Flags;
-use crate::flags::TestFlags;
-use crate::flags::TypeCheckMode;
 use crate::fmt_errors::format_js_error;
 use crate::fs_util::collect_specifiers;
 use crate::fs_util::is_supported_test_ext;
diff --git a/cli/tools/upgrade.rs b/cli/tools/upgrade.rs
index d72fb1b0ae..db1383eb01 100644
--- a/cli/tools/upgrade.rs
+++ b/cli/tools/upgrade.rs
@@ -2,7 +2,7 @@
 
 //! This module provides feature to upgrade deno executable
 
-use crate::flags::UpgradeFlags;
+use crate::args::UpgradeFlags;
 use deno_core::anyhow::bail;
 use deno_core::error::AnyError;
 use deno_core::futures::StreamExt;
diff --git a/cli/tools/vendor/mod.rs b/cli/tools/vendor/mod.rs
index 69c759154b..15b149e2e5 100644
--- a/cli/tools/vendor/mod.rs
+++ b/cli/tools/vendor/mod.rs
@@ -11,8 +11,8 @@ use deno_core::resolve_url_or_path;
 use deno_runtime::permissions::Permissions;
 use log::warn;
 
-use crate::config_file::FmtOptionsConfig;
-use crate::flags::VendorFlags;
+use crate::args::FmtOptionsConfig;
+use crate::args::VendorFlags;
 use crate::fs_util;
 use crate::fs_util::relative_specifier;
 use crate::fs_util::specifier_to_file_path;
diff --git a/cli/tsc.rs b/cli/tsc.rs
index b293ea3b2c..95fdd305a1 100644
--- a/cli/tsc.rs
+++ b/cli/tsc.rs
@@ -1,6 +1,6 @@
 // Copyright 2018-2022 the Deno authors. All rights reserved. MIT license.
 
-use crate::config_file::TsConfig;
+use crate::args::TsConfig;
 use crate::diagnostics::Diagnostics;
 use crate::emit;
 use crate::graph_util::GraphData;
@@ -699,7 +699,7 @@ pub fn exec(request: Request) -> Result<Response, AnyError> {
 #[cfg(test)]
 mod tests {
   use super::*;
-  use crate::config_file::TsConfig;
+  use crate::args::TsConfig;
   use crate::diagnostics::Diagnostic;
   use crate::diagnostics::DiagnosticCategory;
   use crate::emit::Stats;