diff --git a/Cargo.lock b/Cargo.lock
index 8daaa4551c..04be7a90fc 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1307,9 +1307,9 @@ dependencies = [
 
 [[package]]
 name = "deno_config"
-version = "0.20.0"
+version = "0.20.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "64772162a8e8c1b3a9c48b4a0924e29f5b8f0ae23ea2027361937e96d04d493d"
+checksum = "ff203375858a92c7afa82324e89ff1f84c04fb456613135c4abccc6b8f31e8e5"
 dependencies = [
  "anyhow",
  "deno_semver",
diff --git a/Cargo.toml b/Cargo.toml
index 2e5464718f..439ec744aa 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -101,7 +101,7 @@ console_static_text = "=0.8.1"
 data-encoding = "2.3.3"
 data-url = "=0.3.0"
 deno_cache_dir = "=0.10.0"
-deno_config = { version = "=0.20.0", default-features = false }
+deno_config = { version = "=0.20.1", default-features = false }
 dlopen2 = "0.6.1"
 ecb = "=0.1.2"
 elliptic-curve = { version = "0.13.4", features = ["alloc", "arithmetic", "ecdh", "std", "pem"] }
diff --git a/cli/args/flags.rs b/cli/args/flags.rs
index b68b4aadb7..89f53d5937 100644
--- a/cli/args/flags.rs
+++ b/cli/args/flags.rs
@@ -25,6 +25,7 @@ use log::debug;
 use log::Level;
 use serde::Deserialize;
 use serde::Serialize;
+use std::collections::HashSet;
 use std::env;
 use std::ffi::OsString;
 use std::net::SocketAddr;
@@ -36,7 +37,6 @@ use std::path::PathBuf;
 use std::str::FromStr;
 
 use crate::args::resolve_no_prompt;
-use crate::util::collections::CheckedSet;
 use crate::util::fs::canonicalize_path;
 
 use super::flags_net;
@@ -865,20 +865,20 @@ impl Flags {
     args
   }
 
-  /// Extract the directory paths the config file should be discovered from.
+  /// Extract the paths the config file should be discovered from.
   ///
   /// Returns `None` if the config file should not be auto-discovered.
   pub fn config_path_args(&self, current_dir: &Path) -> Option<Vec<PathBuf>> {
     fn resolve_multiple_files(
-      files: &[String],
+      files_or_dirs: &[String],
       current_dir: &Path,
     ) -> Vec<PathBuf> {
-      let mut seen = CheckedSet::with_capacity(files.len());
-      let result = files
+      let mut seen = HashSet::with_capacity(files_or_dirs.len());
+      let result = files_or_dirs
         .iter()
         .filter_map(|p| {
-          let path = normalize_path(current_dir.join(p).parent()?);
-          if seen.insert(&path) {
+          let path = normalize_path(current_dir.join(p));
+          if seen.insert(path.clone()) {
             Some(path)
           } else {
             None
@@ -9298,7 +9298,7 @@ mod tests {
         .unwrap();
     assert_eq!(
       flags.config_path_args(&cwd),
-      Some(vec![cwd.join("dir/a/"), cwd.join("dir/b/")])
+      Some(vec![cwd.join("dir/a/a.js"), cwd.join("dir/b/b.js")])
     );
 
     let flags = flags_from_vec(svec!["deno", "lint"]).unwrap();
@@ -9314,7 +9314,11 @@ mod tests {
     .unwrap();
     assert_eq!(
       flags.config_path_args(&cwd),
-      Some(vec![cwd.join("dir/a/"), cwd.join("dir/")])
+      Some(vec![
+        cwd.join("dir/a/a.js"),
+        cwd.join("dir/a/a2.js"),
+        cwd.join("dir/b.js")
+      ])
     );
   }
 
diff --git a/cli/args/mod.rs b/cli/args/mod.rs
index a54003277a..950ba72e25 100644
--- a/cli/args/mod.rs
+++ b/cli/args/mod.rs
@@ -83,7 +83,6 @@ use crate::file_fetcher::FileFetcher;
 use crate::util::fs::canonicalize_path_maybe_not_exists;
 use crate::version;
 
-use deno_config::glob::PathOrPatternSet;
 use deno_config::FmtConfig;
 use deno_config::LintConfig;
 use deno_config::TestConfig;
@@ -274,18 +273,11 @@ pub struct BenchOptions {
 }
 
 impl BenchOptions {
-  pub fn resolve(
-    bench_config: BenchConfig,
-    bench_flags: &BenchFlags,
-    maybe_flags_base: Option<&Path>,
-  ) -> Result<Self, AnyError> {
-    Ok(Self {
-      files: resolve_files(
-        bench_config.files,
-        &bench_flags.files,
-        maybe_flags_base,
-      )?,
-    })
+  pub fn resolve(bench_config: BenchConfig, _bench_flags: &BenchFlags) -> Self {
+    // this is the same, but keeping the same pattern as everywhere else for the future
+    Self {
+      files: bench_config.files,
+    }
   }
 }
 
@@ -309,19 +301,11 @@ impl FmtOptions {
     }
   }
 
-  pub fn resolve(
-    fmt_config: FmtConfig,
-    fmt_flags: &FmtFlags,
-    maybe_flags_base: Option<&Path>,
-  ) -> Result<Self, AnyError> {
-    Ok(Self {
+  pub fn resolve(fmt_config: FmtConfig, fmt_flags: &FmtFlags) -> Self {
+    Self {
       options: resolve_fmt_options(fmt_flags, fmt_config.options),
-      files: resolve_files(
-        fmt_config.files,
-        &fmt_flags.files,
-        maybe_flags_base,
-      )?,
-    })
+      files: fmt_config.files,
+    }
   }
 }
 
@@ -401,18 +385,11 @@ pub struct TestOptions {
 }
 
 impl TestOptions {
-  pub fn resolve(
-    test_config: TestConfig,
-    test_flags: TestFlags,
-    maybe_flags_base: Option<&Path>,
-  ) -> Result<Self, AnyError> {
-    Ok(Self {
-      files: resolve_files(
-        test_config.files,
-        &test_flags.files,
-        maybe_flags_base,
-      )?,
-    })
+  pub fn resolve(test_config: TestConfig, _test_flags: &TestFlags) -> Self {
+    // this is the same, but keeping the same pattern as everywhere else for the future
+    Self {
+      files: test_config.files,
+    }
   }
 }
 
@@ -482,25 +459,17 @@ impl LintOptions {
     }
   }
 
-  pub fn resolve(
-    lint_config: LintConfig,
-    lint_flags: LintFlags,
-    maybe_flags_base: Option<&Path>,
-  ) -> Result<Self, AnyError> {
-    Ok(Self {
-      files: resolve_files(
-        lint_config.files,
-        &lint_flags.files,
-        maybe_flags_base,
-      )?,
+  pub fn resolve(lint_config: LintConfig, lint_flags: &LintFlags) -> Self {
+    Self {
+      files: lint_config.files,
       rules: resolve_lint_rules_options(
-        lint_config.rules,
-        lint_flags.maybe_rules_tags,
-        lint_flags.maybe_rules_include,
-        lint_flags.maybe_rules_exclude,
+        lint_config.options.rules,
+        lint_flags.maybe_rules_tags.clone(),
+        lint_flags.maybe_rules_include.clone(),
+        lint_flags.maybe_rules_exclude.clone(),
       ),
       fix: lint_flags.fix,
-    })
+    }
   }
 }
 
@@ -907,9 +876,9 @@ impl CliOptions {
 
     let workspace = match &flags.config_flag {
       deno_config::ConfigFlag::Discover => {
-        if let Some(start_dirs) = flags.config_path_args(&initial_cwd) {
+        if let Some(start_paths) = flags.config_path_args(&initial_cwd) {
           Workspace::discover(
-            WorkspaceDiscoverStart::Dirs(&start_dirs),
+            WorkspaceDiscoverStart::Paths(&start_paths),
             &resolve_workspace_discover_options(),
           )?
         } else {
@@ -1355,28 +1324,20 @@ impl CliOptions {
   pub fn resolve_fmt_options_for_members(
     &self,
     fmt_flags: &FmtFlags,
-  ) -> Result<Vec<FmtOptions>, AnyError> {
+  ) -> Result<Vec<(WorkspaceMemberContext, FmtOptions)>, AnyError> {
     let cli_arg_patterns =
       fmt_flags.files.as_file_patterns(self.initial_cwd())?;
-    let member_ctxs =
-      self.workspace.resolve_ctxs_from_patterns(&cli_arg_patterns);
-    let mut result = Vec::with_capacity(member_ctxs.len());
-    for member_ctx in &member_ctxs {
-      let options = self.resolve_fmt_options(fmt_flags, member_ctx)?;
-      result.push(options);
+    let member_configs = self
+      .workspace
+      .resolve_fmt_config_for_members(&cli_arg_patterns)?;
+    let mut result = Vec::with_capacity(member_configs.len());
+    for (ctx, config) in member_configs {
+      let options = FmtOptions::resolve(config, fmt_flags);
+      result.push((ctx, options));
     }
     Ok(result)
   }
 
-  pub fn resolve_fmt_options(
-    &self,
-    fmt_flags: &FmtFlags,
-    ctx: &WorkspaceMemberContext,
-  ) -> Result<FmtOptions, AnyError> {
-    let fmt_config = ctx.to_fmt_config()?;
-    FmtOptions::resolve(fmt_config, fmt_flags, Some(&self.initial_cwd))
-  }
-
   pub fn resolve_workspace_lint_options(
     &self,
     lint_flags: &LintFlags,
@@ -1391,27 +1352,18 @@ impl CliOptions {
   ) -> Result<Vec<(WorkspaceMemberContext, LintOptions)>, AnyError> {
     let cli_arg_patterns =
       lint_flags.files.as_file_patterns(self.initial_cwd())?;
-    let member_ctxs =
-      self.workspace.resolve_ctxs_from_patterns(&cli_arg_patterns);
-    let mut result = Vec::with_capacity(member_ctxs.len());
-    for member_ctx in member_ctxs {
-      let options =
-        self.resolve_lint_options(lint_flags.clone(), &member_ctx)?;
-      result.push((member_ctx, options));
+    let member_configs = self
+      .workspace
+      .resolve_lint_config_for_members(&cli_arg_patterns)?;
+    let mut result = Vec::with_capacity(member_configs.len());
+    for (ctx, config) in member_configs {
+      let options = LintOptions::resolve(config, lint_flags);
+      result.push((ctx, options));
     }
     Ok(result)
   }
 
-  pub fn resolve_lint_options(
-    &self,
-    lint_flags: LintFlags,
-    ctx: &WorkspaceMemberContext,
-  ) -> Result<LintOptions, AnyError> {
-    let lint_config = ctx.to_lint_config()?;
-    LintOptions::resolve(lint_config, lint_flags, Some(&self.initial_cwd))
-  }
-
-  pub fn resolve_lint_config(
+  pub fn resolve_deno_lint_config(
     &self,
   ) -> Result<deno_lint::linter::LintConfig, AnyError> {
     let ts_config_result =
@@ -1445,12 +1397,12 @@ impl CliOptions {
   ) -> Result<Vec<(WorkspaceMemberContext, TestOptions)>, AnyError> {
     let cli_arg_patterns =
       test_flags.files.as_file_patterns(self.initial_cwd())?;
-    let member_ctxs =
-      self.workspace.resolve_ctxs_from_patterns(&cli_arg_patterns);
+    let member_ctxs = self
+      .workspace
+      .resolve_test_config_for_members(&cli_arg_patterns)?;
     let mut result = Vec::with_capacity(member_ctxs.len());
-    for member_ctx in member_ctxs {
-      let options =
-        self.resolve_test_options(test_flags.clone(), &member_ctx)?;
+    for (member_ctx, config) in member_ctxs {
+      let options = TestOptions::resolve(config, test_flags);
       result.push((member_ctx, options));
     }
     Ok(result)
@@ -1463,40 +1415,23 @@ impl CliOptions {
     WorkspaceBenchOptions::resolve(bench_flags)
   }
 
-  pub fn resolve_test_options(
-    &self,
-    test_flags: TestFlags,
-    ctx: &WorkspaceMemberContext,
-  ) -> Result<TestOptions, AnyError> {
-    let test_config = ctx.to_test_config()?;
-    TestOptions::resolve(test_config, test_flags, Some(&self.initial_cwd))
-  }
-
   pub fn resolve_bench_options_for_members(
     &self,
     bench_flags: &BenchFlags,
   ) -> Result<Vec<(WorkspaceMemberContext, BenchOptions)>, AnyError> {
     let cli_arg_patterns =
       bench_flags.files.as_file_patterns(self.initial_cwd())?;
-    let member_ctxs =
-      self.workspace.resolve_ctxs_from_patterns(&cli_arg_patterns);
+    let member_ctxs = self
+      .workspace
+      .resolve_bench_config_for_members(&cli_arg_patterns)?;
     let mut result = Vec::with_capacity(member_ctxs.len());
-    for member_ctx in member_ctxs {
-      let options = self.resolve_bench_options(bench_flags, &member_ctx)?;
+    for (member_ctx, config) in member_ctxs {
+      let options = BenchOptions::resolve(config, bench_flags);
       result.push((member_ctx, options));
     }
     Ok(result)
   }
 
-  pub fn resolve_bench_options(
-    &self,
-    bench_flags: &BenchFlags,
-    ctx: &WorkspaceMemberContext,
-  ) -> Result<BenchOptions, AnyError> {
-    let bench_config = ctx.to_bench_config()?;
-    BenchOptions::resolve(bench_config, bench_flags, Some(&self.initial_cwd))
-  }
-
   pub fn resolve_deno_graph_workspace_members(
     &self,
   ) -> Result<Vec<deno_graph::WorkspaceMember>, AnyError> {
@@ -1873,31 +1808,6 @@ impl StorageKeyResolver {
   }
 }
 
-/// Collect included and ignored files. CLI flags take precedence
-/// over config file, i.e. if there's `files.ignore` in config file
-/// and `--ignore` CLI flag, only the flag value is taken into account.
-fn resolve_files(
-  mut files_config: FilePatterns,
-  file_flags: &FileFlags,
-  maybe_flags_base: Option<&Path>,
-) -> Result<FilePatterns, AnyError> {
-  if !file_flags.include.is_empty() {
-    files_config.include =
-      Some(PathOrPatternSet::from_include_relative_path_or_patterns(
-        maybe_flags_base.unwrap_or(&files_config.base),
-        &file_flags.include,
-      )?);
-  }
-  if !file_flags.ignore.is_empty() {
-    files_config.exclude =
-      PathOrPatternSet::from_exclude_relative_path_or_patterns(
-        maybe_flags_base.unwrap_or(&files_config.base),
-        &file_flags.ignore,
-      )?;
-  }
-  Ok(files_config)
-}
-
 /// Resolves the no_prompt value based on the cli flags and environment.
 pub fn resolve_no_prompt(flags: &PermissionFlags) -> bool {
   flags.no_prompt || has_flag_env_var("DENO_NO_PROMPT")
@@ -1937,10 +1847,10 @@ pub fn config_to_deno_graph_workspace_member(
 
 #[cfg(test)]
 mod test {
-  use super::*;
-  use deno_config::glob::FileCollector;
   use pretty_assertions::assert_eq;
 
+  use super::*;
+
   #[test]
   fn resolve_import_map_flags_take_precedence() {
     let config_text = r#"{
@@ -2018,95 +1928,6 @@ mod test {
     assert_eq!(resolver.resolve_storage_key(&specifier), None);
   }
 
-  #[test]
-  fn resolve_files_test() {
-    use test_util::TempDir;
-    let temp_dir = TempDir::new();
-
-    temp_dir.create_dir_all("data");
-    temp_dir.create_dir_all("nested");
-    temp_dir.create_dir_all("nested/foo");
-    temp_dir.create_dir_all("nested/fizz");
-    temp_dir.create_dir_all("pages");
-
-    temp_dir.write("data/tes.ts", "");
-    temp_dir.write("data/test1.js", "");
-    temp_dir.write("data/test1.ts", "");
-    temp_dir.write("data/test12.ts", "");
-
-    temp_dir.write("nested/foo/foo.ts", "");
-    temp_dir.write("nested/foo/bar.ts", "");
-    temp_dir.write("nested/foo/fizz.ts", "");
-    temp_dir.write("nested/foo/bazz.ts", "");
-
-    temp_dir.write("nested/fizz/foo.ts", "");
-    temp_dir.write("nested/fizz/bar.ts", "");
-    temp_dir.write("nested/fizz/fizz.ts", "");
-    temp_dir.write("nested/fizz/bazz.ts", "");
-
-    temp_dir.write("pages/[id].ts", "");
-
-    let temp_dir_path = temp_dir.path().as_path();
-    let error = PathOrPatternSet::from_include_relative_path_or_patterns(
-      temp_dir_path,
-      &["data/**********.ts".to_string()],
-    )
-    .unwrap_err();
-    assert!(error.to_string().starts_with("Failed to expand glob"));
-
-    let resolved_files = resolve_files(
-      FilePatterns {
-        base: temp_dir_path.to_path_buf(),
-        include: Some(
-          PathOrPatternSet::from_include_relative_path_or_patterns(
-            temp_dir_path,
-            &[
-              "data/test1.?s".to_string(),
-              "nested/foo/*.ts".to_string(),
-              "nested/fizz/*.ts".to_string(),
-              "pages/[id].ts".to_string(),
-            ],
-          )
-          .unwrap(),
-        ),
-        exclude: PathOrPatternSet::from_exclude_relative_path_or_patterns(
-          temp_dir_path,
-          &["nested/**/*bazz.ts".to_string()],
-        )
-        .unwrap(),
-      },
-      &Default::default(),
-      Some(temp_dir_path),
-    )
-    .unwrap();
-
-    let mut files = FileCollector::new(|_| true)
-      .ignore_git_folder()
-      .ignore_node_modules()
-      .collect_file_patterns(&deno_config::fs::RealDenoConfigFs, resolved_files)
-      .unwrap();
-
-    files.sort();
-
-    assert_eq!(
-      files,
-      vec![
-        "data/test1.js",
-        "data/test1.ts",
-        "nested/fizz/bar.ts",
-        "nested/fizz/fizz.ts",
-        "nested/fizz/foo.ts",
-        "nested/foo/bar.ts",
-        "nested/foo/fizz.ts",
-        "nested/foo/foo.ts",
-        "pages/[id].ts",
-      ]
-      .into_iter()
-      .map(|p| deno_core::normalize_path(temp_dir_path.join(p)))
-      .collect::<Vec<_>>()
-    );
-  }
-
   #[test]
   fn jsr_urls() {
     let reg_url = jsr_url();
diff --git a/cli/lsp/config.rs b/cli/lsp/config.rs
index 3c360b683b..3fded336b6 100644
--- a/cli/lsp/config.rs
+++ b/cli/lsp/config.rs
@@ -1232,7 +1232,7 @@ impl ConfigData {
         .and_then(|config_file| {
           config_file
             .to_fmt_config()
-            .and_then(|o| FmtOptions::resolve(o, &Default::default(), None))
+            .map(|o| FmtOptions::resolve(o, &Default::default()))
             .inspect_err(|err| {
               lsp_warn!("  Couldn't read formatter configuration: {}", err)
             })
@@ -1260,7 +1260,7 @@ impl ConfigData {
         .and_then(|config_file| {
           config_file
             .to_lint_config()
-            .and_then(|o| LintOptions::resolve(o, Default::default(), None))
+            .map(|o| LintOptions::resolve(o, &Default::default()))
             .inspect_err(|err| {
               lsp_warn!("  Couldn't read lint configuration: {}", err)
             })
diff --git a/cli/lsp/language_server.rs b/cli/lsp/language_server.rs
index b3deef35bb..093ea1dab2 100644
--- a/cli/lsp/language_server.rs
+++ b/cli/lsp/language_server.rs
@@ -3557,7 +3557,7 @@ impl Inner {
       .unwrap_or_else(|| self.initial_cwd.clone());
     // todo: we need a way to convert config data to a Workspace
     let workspace = Arc::new(Workspace::discover(
-      deno_config::workspace::WorkspaceDiscoverStart::Dirs(&[
+      deno_config::workspace::WorkspaceDiscoverStart::Paths(&[
         initial_cwd.clone()
       ]),
       &WorkspaceDiscoverOptions {
diff --git a/cli/tools/fmt.rs b/cli/tools/fmt.rs
index 9a21b4c105..040991e7c2 100644
--- a/cli/tools/fmt.rs
+++ b/cli/tools/fmt.rs
@@ -53,8 +53,9 @@ pub async fn format(flags: Flags, fmt_flags: FmtFlags) -> Result<(), AnyError> {
   if fmt_flags.is_stdin() {
     let cli_options = CliOptions::from_flags(flags)?;
     let start_ctx = cli_options.workspace.resolve_start_ctx();
-    let fmt_options =
-      cli_options.resolve_fmt_options(&fmt_flags, &start_ctx)?;
+    let fmt_config = start_ctx
+      .to_fmt_config(FilePatterns::new_with_base(start_ctx.dir_path()))?;
+    let fmt_options = FmtOptions::resolve(fmt_config, &fmt_flags);
     return format_stdin(
       &fmt_flags,
       fmt_options,
@@ -143,7 +144,7 @@ fn resolve_paths_with_options_batches(
     cli_options.resolve_fmt_options_for_members(fmt_flags)?;
   let mut paths_with_options_batches =
     Vec::with_capacity(members_fmt_options.len());
-  for member_fmt_options in members_fmt_options {
+  for (_ctx, member_fmt_options) in members_fmt_options {
     let files =
       collect_fmt_files(cli_options, member_fmt_options.files.clone())?;
     if !files.is_empty() {
diff --git a/cli/tools/lint/mod.rs b/cli/tools/lint/mod.rs
index 606d5835cb..2754262657 100644
--- a/cli/tools/lint/mod.rs
+++ b/cli/tools/lint/mod.rs
@@ -91,7 +91,7 @@ pub async fn lint(flags: Flags, lint_flags: LintFlags) -> Result<(), AnyError> {
         Ok(async move {
           let factory = CliFactory::from_flags(flags)?;
           let cli_options = factory.cli_options();
-          let lint_config = cli_options.resolve_lint_config()?;
+          let lint_config = cli_options.resolve_deno_lint_config()?;
           let mut paths_with_options_batches =
             resolve_paths_with_options_batches(cli_options, &lint_flags)?;
           for paths_with_options in &mut paths_with_options_batches {
@@ -143,7 +143,7 @@ pub async fn lint(flags: Flags, lint_flags: LintFlags) -> Result<(), AnyError> {
     let factory = CliFactory::from_flags(flags)?;
     let cli_options = factory.cli_options();
     let is_stdin = lint_flags.is_stdin();
-    let lint_config = cli_options.resolve_lint_config()?;
+    let deno_lint_config = cli_options.resolve_deno_lint_config()?;
     let workspace_lint_options =
       cli_options.resolve_workspace_lint_options(&lint_flags)?;
     let success = if is_stdin {
@@ -151,14 +151,15 @@ pub async fn lint(flags: Flags, lint_flags: LintFlags) -> Result<(), AnyError> {
       let reporter_lock = Arc::new(Mutex::new(create_reporter(
         workspace_lint_options.reporter_kind,
       )));
-      let lint_options =
-        cli_options.resolve_lint_options(lint_flags, &start_ctx)?;
+      let lint_config = start_ctx
+        .to_lint_config(FilePatterns::new_with_base(start_ctx.dir_path()))?;
+      let lint_options = LintOptions::resolve(lint_config, &lint_flags);
       let lint_rules = get_config_rules_err_empty(
         lint_options.rules,
         start_ctx.maybe_deno_json().map(|c| c.as_ref()),
       )?;
       let file_path = cli_options.initial_cwd().join(STDIN_FILE_NAME);
-      let r = lint_stdin(&file_path, lint_rules.rules, lint_config);
+      let r = lint_stdin(&file_path, lint_rules.rules, deno_lint_config);
       let success = handle_lint_result(
         &file_path.to_string_lossy(),
         r,
@@ -179,7 +180,7 @@ pub async fn lint(flags: Flags, lint_flags: LintFlags) -> Result<(), AnyError> {
         linter
           .lint_files(
             paths_with_options.options,
-            lint_config.clone(),
+            deno_lint_config.clone(),
             paths_with_options.ctx,
             paths_with_options.paths,
           )
@@ -618,7 +619,7 @@ fn apply_lint_fixes(
 fn lint_stdin(
   file_path: &Path,
   lint_rules: Vec<&'static dyn LintRule>,
-  config: LintConfig,
+  deno_lint_config: LintConfig,
 ) -> Result<(ParsedSource, Vec<LintDiagnostic>), AnyError> {
   let mut source_code = String::new();
   if stdin().read_to_string(&mut source_code).is_err() {
@@ -632,7 +633,7 @@ fn lint_stdin(
       specifier: specifier_from_file_path(file_path)?,
       source_code: deno_ast::strip_bom(source_code),
       media_type: MediaType::TypeScript,
-      config,
+      config: deno_lint_config,
     })
     .map_err(AnyError::from)
 }
diff --git a/cli/util/collections.rs b/cli/util/collections.rs
deleted file mode 100644
index 21f73024b1..0000000000
--- a/cli/util/collections.rs
+++ /dev/null
@@ -1,38 +0,0 @@
-// Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
-
-use std::marker::PhantomData;
-
-pub struct CheckedSet<T: std::hash::Hash + ?Sized> {
-  _kind: PhantomData<T>,
-  checked: std::collections::HashSet<u64>,
-}
-
-impl<T: std::hash::Hash + ?Sized> Default for CheckedSet<T> {
-  fn default() -> Self {
-    Self {
-      _kind: Default::default(),
-      checked: Default::default(),
-    }
-  }
-}
-
-impl<T: std::hash::Hash + ?Sized> CheckedSet<T> {
-  pub fn with_capacity(capacity: usize) -> Self {
-    Self {
-      _kind: PhantomData,
-      checked: std::collections::HashSet::with_capacity(capacity),
-    }
-  }
-
-  pub fn insert(&mut self, value: &T) -> bool {
-    self.checked.insert(self.get_hash(value))
-  }
-
-  fn get_hash(&self, value: &T) -> u64 {
-    use std::collections::hash_map::DefaultHasher;
-    use std::hash::Hasher;
-    let mut hasher = DefaultHasher::new();
-    value.hash(&mut hasher);
-    hasher.finish()
-  }
-}
diff --git a/cli/util/mod.rs b/cli/util/mod.rs
index 2b6583fbc5..b7eef95d3a 100644
--- a/cli/util/mod.rs
+++ b/cli/util/mod.rs
@@ -2,7 +2,6 @@
 
 // Note: Only add code in this folder that has no application specific logic
 pub mod checksum;
-pub mod collections;
 pub mod console;
 pub mod diff;
 pub mod display;