feat(cli): flatten deno.json configuaration (#17799)

28 files changed, 535 insertions, 149 deletions

diff --git a/cli/args/config_file.rs b/cli/args/config_file.rs
index 0dda0db7d..2855199b9 100644
--- a/cli/args/config_file.rs
+++ b/cli/args/config_file.rs
@@ -279,7 +279,7 @@ impl Serialize for TsConfig {
   }
 }
 
-#[derive(Clone, Debug, Default, Deserialize)]
+#[derive(Clone, Debug, Default, Deserialize, PartialEq)]
 #[serde(default, deny_unknown_fields)]
 pub struct LintRulesConfig {
   pub tags: Option<Vec<String>>,
@@ -287,7 +287,7 @@ pub struct LintRulesConfig {
   pub exclude: Option<Vec<String>>,
 }
 
-#[derive(Clone, Debug, Default, Deserialize)]
+#[derive(Clone, Debug, Default, Deserialize, PartialEq)]
 #[serde(default, deny_unknown_fields)]
 struct SerializedFilesConfig {
   pub include: Vec<String>,
@@ -319,6 +319,10 @@ impl SerializedFilesConfig {
         .collect::<Result<Vec<_>, _>>()?,
     })
   }
+
+  pub fn is_empty(&self) -> bool {
+    self.include.is_empty() && self.exclude.is_empty()
+  }
 }
 
 #[derive(Clone, Debug, Default, Eq, PartialEq)]
@@ -346,11 +350,57 @@ impl FilesConfig {
   }
 }
 
-#[derive(Clone, Debug, Default, Deserialize)]
+/// Choose between flat and nested files configuration.
+///
+/// `files` has precedence over `deprecated_files`.
+/// when `deprecated_files` is present, a warning is logged.
+///
+/// caveat: due to default values, it's not possible to distinguish between
+/// an empty configuration and a configuration with default values.
+/// `{ "files": {} }` is equivalent to `{ "files": { "include": [], "exclude": [] } }`
+/// and it wouldn't be able to emit warning for `{ "files": {}, "exclude": [] }`.
+///
+/// # Arguments
+///
+/// * `files` - Flat configuration.
+/// * `deprecated_files` - Nested configuration. ("Files")
+fn choose_files(
+  files: SerializedFilesConfig,
+  deprecated_files: SerializedFilesConfig,
+) -> SerializedFilesConfig {
+  const DEPRECATED_FILES: &str =
+    "Warning: \"files\" configuration is deprecated";
+  const FLAT_CONFIG: &str = "\"include\" and \"exclude\"";
+
+  let (files_nonempty, deprecated_files_nonempty) =
+    (!files.is_empty(), !deprecated_files.is_empty());
+
+  match (files_nonempty, deprecated_files_nonempty) {
+    (true, true) => {
+      log::warn!("{DEPRECATED_FILES} and ignored by {FLAT_CONFIG}.");
+      files
+    }
+    (true, false) => files,
+    (false, true) => {
+      log::warn!("{DEPRECATED_FILES}. Please use {FLAT_CONFIG} instead.");
+      deprecated_files
+    }
+    (false, false) => SerializedFilesConfig::default(),
+  }
+}
+
+/// `lint` config representation for serde
+///
+/// fields `include` and `exclude` are expanded from [SerializedFilesConfig].
+#[derive(Clone, Debug, Default, Deserialize, PartialEq)]
 #[serde(default, deny_unknown_fields)]
 struct SerializedLintConfig {
   pub rules: LintRulesConfig,
-  pub files: SerializedFilesConfig,
+  pub include: Vec<String>,
+  pub exclude: Vec<String>,
+
+  #[serde(rename = "files")]
+  pub deprecated_files: SerializedFilesConfig,
   pub report: Option<String>,
 }
 
@@ -359,22 +409,26 @@ impl SerializedLintConfig {
     self,
     config_file_specifier: &ModuleSpecifier,
   ) -> Result<LintConfig, AnyError> {
+    let (include, exclude) = (self.include, self.exclude);
+    let files = SerializedFilesConfig { include, exclude };
+
     Ok(LintConfig {
       rules: self.rules,
-      files: self.files.into_resolved(config_file_specifier)?,
+      files: choose_files(files, self.deprecated_files)
+        .into_resolved(config_file_specifier)?,
       report: self.report,
     })
   }
 }
 
-#[derive(Clone, Debug, Default)]
+#[derive(Clone, Debug, Default, PartialEq)]
 pub struct LintConfig {
   pub rules: LintRulesConfig,
   pub files: FilesConfig,
   pub report: Option<String>,
 }
 
-#[derive(Clone, Copy, Debug, Serialize, Deserialize)]
+#[derive(Clone, Copy, Debug, Serialize, Deserialize, PartialEq)]
 #[serde(deny_unknown_fields, rename_all = "camelCase")]
 pub enum ProseWrap {
   Always,
@@ -382,7 +436,7 @@ pub enum ProseWrap {
   Preserve,
 }
 
-#[derive(Clone, Debug, Default, Serialize, Deserialize)]
+#[derive(Clone, Debug, Default, Serialize, Deserialize, PartialEq)]
 #[serde(default, deny_unknown_fields, rename_all = "camelCase")]
 pub struct FmtOptionsConfig {
   pub use_tabs: Option<bool>,
@@ -393,11 +447,75 @@ pub struct FmtOptionsConfig {
   pub semi_colons: Option<bool>,
 }
 
-#[derive(Clone, Debug, Default, Deserialize)]
-#[serde(default, deny_unknown_fields)]
+impl FmtOptionsConfig {
+  pub fn is_empty(&self) -> bool {
+    self.use_tabs.is_none()
+      && self.line_width.is_none()
+      && self.indent_width.is_none()
+      && self.single_quote.is_none()
+      && self.prose_wrap.is_none()
+      && self.semi_colons.is_none()
+  }
+}
+
+/// Choose between flat and nested fmt options.
+///
+/// `options` has precedence over `deprecated_options`.
+/// when `deprecated_options` is present, a warning is logged.
+///
+/// caveat: due to default values, it's not possible to distinguish between
+/// an empty configuration and a configuration with default values.
+/// `{ "fmt": {} } is equivalent to `{ "fmt": { "options": {} } }`
+/// and it wouldn't be able to emit warning for `{ "fmt": { "options": {}, "semiColons": "false" } }`.
+///
+/// # Arguments
+///
+/// * `options` - Flat options.
+/// * `deprecated_options` - Nested files configuration ("option").
+fn choose_fmt_options(
+  options: FmtOptionsConfig,
+  deprecated_options: FmtOptionsConfig,
+) -> FmtOptionsConfig {
+  const DEPRECATED_OPTIONS: &str =
+    "Warning: \"options\" configuration is deprecated";
+  const FLAT_OPTION: &str = "\"flat\" options";
+
+  let (options_nonempty, deprecated_options_nonempty) =
+    (!options.is_empty(), !deprecated_options.is_empty());
+
+  match (options_nonempty, deprecated_options_nonempty) {
+    (true, true) => {
+      log::warn!("{DEPRECATED_OPTIONS} and ignored by {FLAT_OPTION}.");
+      options
+    }
+    (true, false) => options,
+    (false, true) => {
+      log::warn!("{DEPRECATED_OPTIONS}. Please use {FLAT_OPTION} instead.");
+      deprecated_options
+    }
+    (false, false) => FmtOptionsConfig::default(),
+  }
+}
+
+/// `fmt` config representation for serde
+///
+/// fields from `use_tabs`..`semi_colons` are expanded from [FmtOptionsConfig].
+/// fields `include` and `exclude` are expanded from [SerializedFilesConfig].
+#[derive(Clone, Debug, Default, Deserialize, PartialEq)]
+#[serde(default, deny_unknown_fields, rename_all = "camelCase")]
 struct SerializedFmtConfig {
-  pub options: FmtOptionsConfig,
-  pub files: SerializedFilesConfig,
+  pub use_tabs: Option<bool>,
+  pub line_width: Option<u32>,
+  pub indent_width: Option<u8>,
+  pub single_quote: Option<bool>,
+  pub prose_wrap: Option<ProseWrap>,
+  pub semi_colons: Option<bool>,
+  #[serde(rename = "options")]
+  pub deprecated_options: FmtOptionsConfig,
+  pub include: Vec<String>,
+  pub exclude: Vec<String>,
+  #[serde(rename = "files")]
+  pub deprecated_files: SerializedFilesConfig,
 }
 
 impl SerializedFmtConfig {
@@ -405,23 +523,41 @@ impl SerializedFmtConfig {
     self,
     config_file_specifier: &ModuleSpecifier,
   ) -> Result<FmtConfig, AnyError> {
+    let (include, exclude) = (self.include, self.exclude);
+    let files = SerializedFilesConfig { include, exclude };
+    let options = FmtOptionsConfig {
+      use_tabs: self.use_tabs,
+      line_width: self.line_width,
+      indent_width: self.indent_width,
+      single_quote: self.single_quote,
+      prose_wrap: self.prose_wrap,
+      semi_colons: self.semi_colons,
+    };
+
     Ok(FmtConfig {
-      options: self.options,
-      files: self.files.into_resolved(config_file_specifier)?,
+      options: choose_fmt_options(options, self.deprecated_options),
+      files: choose_files(files, self.deprecated_files)
+        .into_resolved(config_file_specifier)?,
     })
   }
 }
 
-#[derive(Clone, Debug, Default)]
+#[derive(Clone, Debug, Default, PartialEq)]
 pub struct FmtConfig {
   pub options: FmtOptionsConfig,
   pub files: FilesConfig,
 }
 
-#[derive(Clone, Debug, Default, Deserialize)]
+/// `test` config representation for serde
+///
+/// fields `include` and `exclude` are expanded from [SerializedFilesConfig].
+#[derive(Clone, Debug, Default, Deserialize, PartialEq)]
 #[serde(default, deny_unknown_fields)]
 struct SerializedTestConfig {
-  pub files: SerializedFilesConfig,
+  pub include: Vec<String>,
+  pub exclude: Vec<String>,
+  #[serde(rename = "files")]
+  pub deprecated_files: SerializedFilesConfig,
 }
 
 impl SerializedTestConfig {
@@ -429,21 +565,31 @@ impl SerializedTestConfig {
     self,
     config_file_specifier: &ModuleSpecifier,
   ) -> Result<TestConfig, AnyError> {
+    let (include, exclude) = (self.include, self.exclude);
+    let files = SerializedFilesConfig { include, exclude };
+
     Ok(TestConfig {
-      files: self.files.into_resolved(config_file_specifier)?,
+      files: choose_files(files, self.deprecated_files)
+        .into_resolved(config_file_specifier)?,
     })
   }
 }
 
-#[derive(Clone, Debug, Default)]
+#[derive(Clone, Debug, Default, PartialEq)]
 pub struct TestConfig {
   pub files: FilesConfig,
 }
 
-#[derive(Clone, Debug, Default, Deserialize)]
+/// `bench` config representation for serde
+///
+/// fields `include` and `exclude` are expanded from [SerializedFilesConfig].
+#[derive(Clone, Debug, Default, Deserialize, PartialEq)]
 #[serde(default, deny_unknown_fields)]
 struct SerializedBenchConfig {
-  pub files: SerializedFilesConfig,
+  pub include: Vec<String>,
+  pub exclude: Vec<String>,
+  #[serde(rename = "files")]
+  pub deprecated_files: SerializedFilesConfig,
 }
 
 impl SerializedBenchConfig {
@@ -451,18 +597,22 @@ impl SerializedBenchConfig {
     self,
     config_file_specifier: &ModuleSpecifier,
   ) -> Result<BenchConfig, AnyError> {
+    let (include, exclude) = (self.include, self.exclude);
+    let files = SerializedFilesConfig { include, exclude };
+
     Ok(BenchConfig {
-      files: self.files.into_resolved(config_file_specifier)?,
+      files: choose_files(files, self.deprecated_files)
+        .into_resolved(config_file_specifier)?,
     })
   }
 }
 
-#[derive(Clone, Debug, Default)]
+#[derive(Clone, Debug, Default, PartialEq)]
 pub struct BenchConfig {
   pub files: FilesConfig,
 }
 
-#[derive(Clone, Debug, Deserialize)]
+#[derive(Clone, Debug, Deserialize, PartialEq)]
 #[serde(untagged)]
 pub enum LockConfig {
   Bool(bool),
@@ -999,6 +1149,12 @@ mod tests {
   use deno_core::serde_json::json;
   use pretty_assertions::assert_eq;
 
+  fn unpack_object<T>(result: Result<Option<T>, AnyError>, name: &str) -> T {
+    result
+      .unwrap_or_else(|err| panic!("error parsing {name} object but got {err}"))
+      .unwrap_or_else(|| panic!("{name} object should be defined"))
+  }
+
   #[test]
   fn read_config_file_absolute() {
     let path = test_util::testdata_path().join("module_graph/tsconfig.json");
@@ -1043,27 +1199,21 @@ mod tests {
         "strict": true
       },
       "lint": {
-        "files": {
-          "include": ["src/"],
-          "exclude": ["src/testdata/"]
-        },
+        "include": ["src/"],
+        "exclude": ["src/testdata/"],
         "rules": {
           "tags": ["recommended"],
           "include": ["ban-untagged-todo"]
         }
       },
       "fmt": {
-        "files": {
-          "include": ["src/"],
-          "exclude": ["src/testdata/"]
-        },
-        "options": {
-          "useTabs": true,
-          "lineWidth": 80,
-          "indentWidth": 4,
-          "singleQuote": true,
-          "proseWrap": "preserve"
-        }
+        "include": ["src/"],
+        "exclude": ["src/testdata/"],
+        "useTabs": true,
+        "lineWidth": 80,
+        "indentWidth": 4,
+        "singleQuote": true,
+        "proseWrap": "preserve"
       },
       "tasks": {
         "build": "deno run --allow-read --allow-write build.ts",
@@ -1087,38 +1237,38 @@ mod tests {
       }),
     );
 
-    let lint_config = config_file
-      .to_lint_config()
-      .expect("error parsing lint object")
-      .expect("lint object should be defined");
-    assert_eq!(lint_config.files.include, vec![PathBuf::from("/deno/src/")]);
     assert_eq!(
-      lint_config.files.exclude,
-      vec![PathBuf::from("/deno/src/testdata/")]
-    );
-    assert_eq!(
-      lint_config.rules.include,
-      Some(vec!["ban-untagged-todo".to_string()])
-    );
-    assert_eq!(
-      lint_config.rules.tags,
-      Some(vec!["recommended".to_string()])
+      unpack_object(config_file.to_lint_config(), "lint"),
+      LintConfig {
+        files: FilesConfig {
+          include: vec![PathBuf::from("/deno/src/")],
+          exclude: vec![PathBuf::from("/deno/src/testdata/")],
+        },
+        rules: LintRulesConfig {
+          include: Some(vec!["ban-untagged-todo".to_string()]),
+          exclude: None,
+          tags: Some(vec!["recommended".to_string()]),
+        },
+        ..Default::default()
+      }
     );
-    assert!(lint_config.rules.exclude.is_none());
-
-    let fmt_config = config_file
-      .to_fmt_config()
-      .expect("error parsing fmt object")
-      .expect("fmt object should be defined");
-    assert_eq!(fmt_config.files.include, vec![PathBuf::from("/deno/src/")]);
     assert_eq!(
-      fmt_config.files.exclude,
-      vec![PathBuf::from("/deno/src/testdata/")],
+      unpack_object(config_file.to_fmt_config(), "fmt"),
+      FmtConfig {
+        files: FilesConfig {
+          include: vec![PathBuf::from("/deno/src/")],
+          exclude: vec![PathBuf::from("/deno/src/testdata/")],
+        },
+        options: FmtOptionsConfig {
+          use_tabs: Some(true),
+          line_width: Some(80),
+          indent_width: Some(4),
+          single_quote: Some(true),
+          prose_wrap: Some(ProseWrap::Preserve),
+          ..Default::default()
+        },
+      }
     );
-    assert_eq!(fmt_config.options.use_tabs, Some(true));
-    assert_eq!(fmt_config.options.line_width, Some(80));
-    assert_eq!(fmt_config.options.indent_width, Some(4));
-    assert_eq!(fmt_config.options.single_quote, Some(true));
 
     let tasks_config = config_file.to_tasks_config().unwrap().unwrap();
     assert_eq!(
@@ -1131,6 +1281,128 @@ mod tests {
     );
   }
 
+  /// if either "include" or "exclude" is specified, "files" is ignored
+  #[test]
+  fn test_parse_config_with_deprecated_files_field() {
+    let config_text = r#"{
+      "lint": {
+        "files": { "include": ["foo/"], "exclude": ["bar/"] },
+        "include": ["src/"]
+      },
+      "fmt": {
+        "files": { "include": ["foo/"], "exclude": ["bar/"] },
+        "exclude": ["dist/"]
+      },
+      "bench": {
+        "files": { "include": ["foo/"] },
+        "include": ["src/"]
+      },
+      "test": {
+        "files": { "include": ["foo/"] },
+        "include": ["src/"]
+      }
+    }"#;
+    let config_dir = ModuleSpecifier::parse("file:///deno/").unwrap();
+    let config_specifier = config_dir.join("tsconfig.json").unwrap();
+    let config_file = ConfigFile::new(config_text, &config_specifier).unwrap();
+
+    let lint_files = unpack_object(config_file.to_lint_config(), "lint").files;
+    assert_eq!(
+      lint_files,
+      FilesConfig {
+        include: vec![PathBuf::from("/deno/src/")],
+        exclude: vec![],
+      }
+    );
+
+    let fmt_files = unpack_object(config_file.to_fmt_config(), "fmt").files;
+    assert_eq!(
+      fmt_files,
+      FilesConfig {
+        exclude: vec![PathBuf::from("/deno/dist/")],
+        include: vec![],
+      }
+    );
+
+    let test_include = unpack_object(config_file.to_test_config(), "test")
+      .files
+      .include;
+    assert_eq!(test_include, vec![PathBuf::from("/deno/src/")]);
+
+    let bench_include = unpack_object(config_file.to_bench_config(), "bench")
+      .files
+      .include;
+    assert_eq!(bench_include, vec![PathBuf::from("/deno/src/")]);
+  }
+
+  #[test]
+  fn test_parse_config_with_deprecated_files_field_only() {
+    let config_text = r#"{
+      "lint": { "files": { "include": ["src/"] } },
+      "fmt": { "files": { "include": ["src/"] } },
+      "test": { "files": { "exclude": ["dist/"] } },
+      "bench": { "files": { "exclude": ["dist/"] } }
+    }"#;
+    let config_dir = ModuleSpecifier::parse("file:///deno/").unwrap();
+    let config_specifier = config_dir.join("tsconfig.json").unwrap();
+    let config_file = ConfigFile::new(config_text, &config_specifier).unwrap();
+
+    let lint_include = unpack_object(config_file.to_lint_config(), "lint")
+      .files
+      .include;
+    assert_eq!(lint_include, vec![PathBuf::from("/deno/src/")]);
+
+    let fmt_include = unpack_object(config_file.to_fmt_config(), "fmt")
+      .files
+      .include;
+    assert_eq!(fmt_include, vec![PathBuf::from("/deno/src/")]);
+
+    let test_exclude = unpack_object(config_file.to_test_config(), "test")
+      .files
+      .exclude;
+    assert_eq!(test_exclude, vec![PathBuf::from("/deno/dist/")]);
+
+    let bench_exclude = unpack_object(config_file.to_bench_config(), "bench")
+      .files
+      .exclude;
+    assert_eq!(bench_exclude, vec![PathBuf::from("/deno/dist/")]);
+  }
+
+  #[test]
+  fn test_parse_config_with_deprecated_fmt_options() {
+    let config_text_both = r#"{
+      "fmt": {
+        "options": {
+          "semiColons": true
+        },
+        "semiColons": false
+      }
+    }"#;
+    let config_text_deprecated = r#"{
+      "fmt": {
+        "options": {
+          "semiColons": true
+        }
+      }
+    }"#;
+    let config_specifier =
+      ModuleSpecifier::parse("file:///deno/tsconfig.json").unwrap();
+    let config_file_both =
+      ConfigFile::new(config_text_both, &config_specifier).unwrap();
+    let config_file_deprecated =
+      ConfigFile::new(config_text_deprecated, &config_specifier).unwrap();
+
+    fn unpack_options(config_file: ConfigFile) -> FmtOptionsConfig {
+      unpack_object(config_file.to_fmt_config(), "fmt").options
+    }
+
+    let fmt_options_both = unpack_options(config_file_both);
+    assert_eq!(fmt_options_both.semi_colons, Some(false));
+
+    let fmt_options_deprecated = unpack_options(config_file_deprecated);
+    assert_eq!(fmt_options_deprecated.semi_colons, Some(true));
+  }
+
   #[test]
   fn test_parse_config_with_empty_file() {
     let config_text = "";
diff --git a/cli/schemas/config-file.v1.json b/cli/schemas/config-file.v1.json
index f0b496720..7978a2597 100644
--- a/cli/schemas/config-file.v1.json
+++ b/cli/schemas/config-file.v1.json
@@ -227,6 +227,20 @@
       "description": "Configuration for linter",
       "type": "object",
       "properties": {
+        "include": {
+          "type": "array",
+          "description": "List of files or directories that will be linted.",
+          "items": {
+            "type": "string"
+          }
+        },
+        "exclude": {
+          "type": "array",
+          "description": "List of files or directories that will not be linted.",
+          "items": {
+            "type": "string"
+          }
+        },
         "files": {
           "type": "object",
           "properties": {
@@ -293,6 +307,20 @@
       "description": "Configuration for formatter",
       "type": "object",
       "properties": {
+        "include": {
+          "type": "array",
+          "description": "List of files or directories that will be formatted.",
+          "items": {
+            "type": "string"
+          }
+        },
+        "exclude": {
+          "type": "array",
+          "description": "List of files or directories that will not be formatted.",
+          "items": {
+            "type": "string"
+          }
+        },
         "files": {
           "type": "object",
           "properties": {
@@ -312,6 +340,40 @@
             }
           }
         },
+        "useTabs": {
+          "description": "Whether to use tabs (true) or spaces (false) for indentation.",
+          "type": "boolean",
+          "default": false
+        },
+        "lineWidth": {
+          "description": "The width of a line the printer will try to stay under. Note that the printer may exceed this width in certain cases.",
+          "type": "number",
+          "default": 80
+        },
+        "indentWidth": {
+          "description": "The number of characters for an indent.",
+          "type": "number",
+          "default": 2
+        },
+        "singleQuote": {
+          "type": "boolean",
+          "description": "Whether to use single quote (true) or double quote (false) for quotation.",
+          "default": false
+        },
+        "proseWrap": {
+          "description": "Define how prose should be wrapped in Markdown files.",
+          "default": "always",
+          "enum": [
+            "always",
+            "never",
+            "preserve"
+          ]
+        },
+        "semiColons": {
+          "description": "Whether to prefer using semicolons.",
+          "type": "boolean",
+          "default": true
+        },
         "options": {
           "type": "object",
           "properties": {
@@ -368,6 +430,20 @@
       "description": "Configuration for deno test",
       "type": "object",
       "properties": {
+        "include": {
+          "type": "array",
+          "description": "List of files or directories that will be searched for tests.",
+          "items": {
+            "type": "string"
+          }
+        },
+        "exclude": {
+          "type": "array",
+          "description": "List of files or directories that will not be searched for tests.",
+          "items": {
+            "type": "string"
+          }
+        },
         "files": {
           "type": "object",
           "properties": {
@@ -393,6 +469,20 @@
       "description": "Configuration for deno bench",
       "type": "object",
       "properties": {
+        "include": {
+          "type": "array",
+          "description": "List of files or directories that will be searched for benchmarks.",
+          "items": {
+            "type": "string"
+          }
+        },
+        "exclude": {
+          "type": "array",
+          "description": "List of files or directories that will not be searched for benchmarks.",
+          "items": {
+            "type": "string"
+          }
+        },
         "files": {
           "type": "object",
           "properties": {
diff --git a/cli/tests/integration/fmt_tests.rs b/cli/tests/integration/fmt_tests.rs
index 7812175a7..e47311cf0 100644
--- a/cli/tests/integration/fmt_tests.rs
+++ b/cli/tests/integration/fmt_tests.rs
@@ -229,6 +229,12 @@ itest!(fmt_with_config {
   output: "fmt/fmt_with_config.out",
 });
 
+itest!(fmt_with_deprecated_config {
+  args:
+    "fmt --config fmt/with_config/deno.deprecated.jsonc fmt/with_config/subdir",
+  output: "fmt/fmt_with_deprecated_config.out",
+});
+
 itest!(fmt_with_config_default {
   args: "fmt fmt/with_config/subdir",
   output: "fmt/fmt_with_config.out",
diff --git a/cli/tests/integration/test_tests.rs b/cli/tests/integration/test_tests.rs
index cf1665289..0e1a39deb 100644
--- a/cli/tests/integration/test_tests.rs
+++ b/cli/tests/integration/test_tests.rs
@@ -77,6 +77,12 @@ itest!(test_with_config2 {
   output: "test/collect2.out",
 });
 
+itest!(test_with_deprecated_config {
+  args: "test --config test/collect/deno.deprecated.jsonc test/collect",
+  exit_code: 0,
+  output: "test/collect.deprecated.out",
+});
+
 itest!(test_with_malformed_config {
   args: "test --config test/collect/deno.malformed.jsonc",
   exit_code: 1,
diff --git a/cli/tests/testdata/bench/collect/deno.jsonc b/cli/tests/testdata/bench/collect/deno.jsonc
index f88d13778..7f8f190d3 100644
--- a/cli/tests/testdata/bench/collect/deno.jsonc
+++ b/cli/tests/testdata/bench/collect/deno.jsonc
@@ -1,7 +1,5 @@
 {
-    "bench": {
-      "files": {
-        "exclude": ["./ignore"]
-      }
-    }
+  "bench": {
+    "exclude": ["./ignore"]
+  }
 }
diff --git a/cli/tests/testdata/bench/collect/deno.malformed.jsonc b/cli/tests/testdata/bench/collect/deno.malformed.jsonc
index 02744bc11..8e558fbcf 100644
--- a/cli/tests/testdata/bench/collect/deno.malformed.jsonc
+++ b/cli/tests/testdata/bench/collect/deno.malformed.jsonc
@@ -1,5 +1,5 @@
 {
-    "bench": {
-      "dont_know_this_field": {}
-    }
+  "bench": {
+    "dont_know_this_field": {}
+  }
 }
diff --git a/cli/tests/testdata/bench/collect/deno2.jsonc b/cli/tests/testdata/bench/collect/deno2.jsonc
index f24da5049..653ab1e31 100644
--- a/cli/tests/testdata/bench/collect/deno2.jsonc
+++ b/cli/tests/testdata/bench/collect/deno2.jsonc
@@ -1,8 +1,6 @@
 {
-    "bench": {
-      "files": {
-        "include": ["./include/"],
-        "exclude": ["./ignore", "./include/2_bench.ts"]
-      }
-    }
+  "bench": {
+    "include": ["./include/"],
+    "exclude": ["./ignore", "./include/2_bench.ts"]
+  }
 }
diff --git a/cli/tests/testdata/bench/collect_with_malformed_config.out b/cli/tests/testdata/bench/collect_with_malformed_config.out
index 10e64707c..92e5e29d2 100644
--- a/cli/tests/testdata/bench/collect_with_malformed_config.out
+++ b/cli/tests/testdata/bench/collect_with_malformed_config.out
@@ -1,4 +1,4 @@
 error: Failed to parse "bench" configuration
 
 Caused by:
-    unknown field `dont_know_this_field`, expected `files`
+    unknown field `dont_know_this_field`, expected one of `include`, `exclude`, `files`
diff --git a/cli/tests/testdata/fmt/deno.malformed.jsonc b/cli/tests/testdata/fmt/deno.malformed.jsonc
index c6200c4ee..e326edb1f 100644
--- a/cli/tests/testdata/fmt/deno.malformed.jsonc
+++ b/cli/tests/testdata/fmt/deno.malformed.jsonc
@@ -1,9 +1,7 @@
 {
   "fmt": {
-    "files": {
-      "include": ["fmt_with_config/"],
-      "exclude": ["fmt_with_config/b.ts"]
-    },
+    "include": ["fmt_with_config/"],
+    "exclude": ["fmt_with_config/b.ts"],
     "dont_know_this_field": {},
     "options": {
       "useTabs": true
diff --git a/cli/tests/testdata/fmt/deno.malformed2.jsonc b/cli/tests/testdata/fmt/deno.malformed2.jsonc
index 4d6e99ae2..e326edb1f 100644
--- a/cli/tests/testdata/fmt/deno.malformed2.jsonc
+++ b/cli/tests/testdata/fmt/deno.malformed2.jsonc
@@ -1,10 +1,8 @@
 {
   "fmt": {
-    "files": {
-      "include": ["fmt_with_config/"],
-      "exclude": ["fmt_with_config/b.ts"],
-      "dont_know_this_field": {}
-    },
+    "include": ["fmt_with_config/"],
+    "exclude": ["fmt_with_config/b.ts"],
+    "dont_know_this_field": {},
     "options": {
       "useTabs": true
     }
diff --git a/cli/tests/testdata/fmt/fmt_with_deprecated_config.out b/cli/tests/testdata/fmt/fmt_with_deprecated_config.out
new file mode 100644
index 000000000..793fac1bc
--- /dev/null
+++ b/cli/tests/testdata/fmt/fmt_with_deprecated_config.out
@@ -0,0 +1,3 @@
+Warning: "options" configuration is deprecated. Please use "flat" options instead.
+Warning: "files" configuration is deprecated. Please use "include" and "exclude" instead.
+Checked 2 files
diff --git a/cli/tests/testdata/fmt/fmt_with_malformed_config.out b/cli/tests/testdata/fmt/fmt_with_malformed_config.out
index 1a55613ef..c269053a6 100644
--- a/cli/tests/testdata/fmt/fmt_with_malformed_config.out
+++ b/cli/tests/testdata/fmt/fmt_with_malformed_config.out
@@ -1,4 +1,4 @@
 error: Failed to parse "fmt" configuration
 
 Caused by:
-    unknown field `dont_know_this_field`, expected `options` or `files`
+    unknown field `dont_know_this_field`, expected one of `useTabs`, `lineWidth`, `indentWidth`, `singleQuote`, `proseWrap`, `semiColons`, `options`, `include`, `exclude`, `files`
diff --git a/cli/tests/testdata/fmt/fmt_with_malformed_config2.out b/cli/tests/testdata/fmt/fmt_with_malformed_config2.out
index 948b6b5b8..c269053a6 100644
--- a/cli/tests/testdata/fmt/fmt_with_malformed_config2.out
+++ b/cli/tests/testdata/fmt/fmt_with_malformed_config2.out
@@ -1,4 +1,4 @@
 error: Failed to parse "fmt" configuration
 
 Caused by:
-    unknown field `dont_know_this_field`, expected `include` or `exclude`
+    unknown field `dont_know_this_field`, expected one of `useTabs`, `lineWidth`, `indentWidth`, `singleQuote`, `proseWrap`, `semiColons`, `options`, `include`, `exclude`, `files`
diff --git a/cli/tests/testdata/fmt/with_config/deno.deprecated.jsonc b/cli/tests/testdata/fmt/with_config/deno.deprecated.jsonc
new file mode 100644
index 000000000..e053233fd
--- /dev/null
+++ b/cli/tests/testdata/fmt/with_config/deno.deprecated.jsonc
@@ -0,0 +1,20 @@
+{
+  "fmt": {
+    "files": {
+      "include": [
+        "./subdir/"
+      ],
+      "exclude": [
+        "./subdir/b.ts"
+      ]
+    },
+    "options": {
+      "useTabs": true,
+      "lineWidth": 40,
+      "indentWidth": 8,
+      "singleQuote": true,
+      "proseWrap": "always",
+      "semiColons": false
+    }
+  }
+}
diff --git a/cli/tests/testdata/fmt/with_config/deno.jsonc b/cli/tests/testdata/fmt/with_config/deno.jsonc
index 44e3f9a99..ffd265dcd 100644
--- a/cli/tests/testdata/fmt/with_config/deno.jsonc
+++ b/cli/tests/testdata/fmt/with_config/deno.jsonc
@@ -1,20 +1,16 @@
 {
 	"fmt": {
-		"files": {
-			"include": [
-				"./subdir/"
-			],
-			"exclude": [
-				"./subdir/b.ts"
-			]
-		},
-		"options": {
-			"useTabs": true,
-			"lineWidth": 40,
-			"indentWidth": 8,
-			"singleQuote": true,
-			"proseWrap": "always",
-			"semiColons": false
-		}
+		"include": [
+			"./subdir/"
+		],
+		"exclude": [
+			"./subdir/b.ts"
+		],
+		"useTabs": true,
+		"lineWidth": 40,
+		"indentWidth": 8,
+		"singleQuote": true,
+		"proseWrap": "always",
+		"semiColons": false
 	}
 }
diff --git a/cli/tests/testdata/lint/Deno.compact.format.jsonc b/cli/tests/testdata/lint/Deno.compact.format.jsonc
index 24b159ca6..f3487501a 100644
--- a/cli/tests/testdata/lint/Deno.compact.format.jsonc
+++ b/cli/tests/testdata/lint/Deno.compact.format.jsonc
@@ -1,9 +1,7 @@
 {
   "lint": {
-    "files": {
-      "include": ["with_config/"],
-      "exclude": ["with_config/b.ts"]
-    },
+    "include": ["with_config/"],
+    "exclude": ["with_config/b.ts"],
     "rules": {
       "tags": ["recommended"],
       "include": ["ban-untagged-todo"]
diff --git a/cli/tests/testdata/lint/Deno.jsonc b/cli/tests/testdata/lint/Deno.jsonc
index 24db221a7..e9c03cca4 100644
--- a/cli/tests/testdata/lint/Deno.jsonc
+++ b/cli/tests/testdata/lint/Deno.jsonc
@@ -1,9 +1,7 @@
 {
   "lint": {
-    "files": {
-      "include": ["with_config/"],
-      "exclude": ["with_config/b.ts"]
-    },
+    "include": ["with_config/"],
+    "exclude": ["with_config/b.ts"],
     "rules": {
       "tags": ["recommended"],
       "include": ["ban-untagged-todo"]
diff --git a/cli/tests/testdata/lint/Deno.malformed.jsonc b/cli/tests/testdata/lint/Deno.malformed.jsonc
index 4534a1fe8..fa71cd851 100644
--- a/cli/tests/testdata/lint/Deno.malformed.jsonc
+++ b/cli/tests/testdata/lint/Deno.malformed.jsonc
@@ -1,9 +1,7 @@
 {
   "lint": {
-    "files": {
-      "include": ["with_config/"],
-      "exclude": ["with_config/b.ts"]
-    },
+    "include": ["with_config/"],
+    "exclude": ["with_config/b.ts"],
     "dont_know_this_field": {},
     "rules": {
       "tags": ["recommended"],
diff --git a/cli/tests/testdata/lint/Deno.malformed2.jsonc b/cli/tests/testdata/lint/Deno.malformed2.jsonc
index 335fcdc23..fa71cd851 100644
--- a/cli/tests/testdata/lint/Deno.malformed2.jsonc
+++ b/cli/tests/testdata/lint/Deno.malformed2.jsonc
@@ -1,10 +1,8 @@
 {
   "lint": {
-    "files": {
-      "include": ["with_config/"],
-      "exclude": ["with_config/b.ts"],
-      "dont_know_this_field": {}
-    },
+    "include": ["with_config/"],
+    "exclude": ["with_config/b.ts"],
+    "dont_know_this_field": {},
     "rules": {
       "tags": ["recommended"],
       "include": ["ban-untagged-todo"]
diff --git a/cli/tests/testdata/lint/Deno.no_tags.jsonc b/cli/tests/testdata/lint/Deno.no_tags.jsonc
index 4771b0b73..b63600a90 100644
--- a/cli/tests/testdata/lint/Deno.no_tags.jsonc
+++ b/cli/tests/testdata/lint/Deno.no_tags.jsonc
@@ -1,13 +1,11 @@
 {
   "lint": {
-    "files": {
-      "include": [
-        "with_config/"
-      ],
-      "exclude": [
-        "with_config/b.ts"
-      ]
-    },
+    "include": [
+      "with_config/"
+    ],
+    "exclude": [
+      "with_config/b.ts"
+    ],
     "rules": {
       "include": [
         "ban-untagged-todo"
diff --git a/cli/tests/testdata/lint/with_malformed_config.out b/cli/tests/testdata/lint/with_malformed_config.out
index 3aa491065..1c0f0fff6 100644
--- a/cli/tests/testdata/lint/with_malformed_config.out
+++ b/cli/tests/testdata/lint/with_malformed_config.out
@@ -1,4 +1,4 @@
 error: Failed to parse "lint" configuration
 
 Caused by:
-    unknown field `dont_know_this_field`, expected one of `rules`, `files`, `report`
+    unknown field `dont_know_this_field`, expected one of `rules`, `include`, `exclude`, `files`, `report`
diff --git a/cli/tests/testdata/lint/with_malformed_config2.out b/cli/tests/testdata/lint/with_malformed_config2.out
index 11e878f00..1c0f0fff6 100644
--- a/cli/tests/testdata/lint/with_malformed_config2.out
+++ b/cli/tests/testdata/lint/with_malformed_config2.out
@@ -1,4 +1,4 @@
 error: Failed to parse "lint" configuration
 
 Caused by:
-    unknown field `dont_know_this_field`, expected `include` or `exclude`
+    unknown field `dont_know_this_field`, expected one of `rules`, `include`, `exclude`, `files`, `report`
diff --git a/cli/tests/testdata/lsp/deno.lint.exclude.jsonc b/cli/tests/testdata/lsp/deno.lint.exclude.jsonc
index 89f6108ec..9d4ba52ad 100644
--- a/cli/tests/testdata/lsp/deno.lint.exclude.jsonc
+++ b/cli/tests/testdata/lsp/deno.lint.exclude.jsonc
@@ -1,10 +1,8 @@
 {
   "lint": {
-    "files": {
-      "exclude": [
-        "ignored.ts"
-      ]
-    },
+    "exclude": [
+      "ignored.ts"
+    ],
     "rules": {
       "exclude": [
         "camelcase"
diff --git a/cli/tests/testdata/test/collect.deprecated.out b/cli/tests/testdata/test/collect.deprecated.out
new file mode 100644
index 000000000..9bf68807c
--- /dev/null
+++ b/cli/tests/testdata/test/collect.deprecated.out
@@ -0,0 +1,10 @@
+Warning: "files" configuration is deprecated. Please use "include" and "exclude" instead.
+Check [WILDCARD]/test/collect/include/2_test.ts
+Check [WILDCARD]/test/collect/include/test.ts
+Check [WILDCARD]/test/collect/test.ts
+running 0 tests from ./test/collect/include/2_test.ts
+running 0 tests from ./test/collect/include/test.ts
+running 0 tests from ./test/collect/test.ts
+
+ok | 0 passed | 0 failed ([WILDCARD])
+
diff --git a/cli/tests/testdata/test/collect/deno.deprecated.jsonc b/cli/tests/testdata/test/collect/deno.deprecated.jsonc
new file mode 100644
index 000000000..b8acda27d
--- /dev/null
+++ b/cli/tests/testdata/test/collect/deno.deprecated.jsonc
@@ -0,0 +1,7 @@
+{
+  "test": {
+    "files": {
+      "exclude": ["./ignore"]
+    }
+  }
+}
diff --git a/cli/tests/testdata/test/collect/deno.jsonc b/cli/tests/testdata/test/collect/deno.jsonc
index b8acda27d..e14ce86da 100644
--- a/cli/tests/testdata/test/collect/deno.jsonc
+++ b/cli/tests/testdata/test/collect/deno.jsonc
@@ -1,7 +1,5 @@
 {
   "test": {
-    "files": {
-      "exclude": ["./ignore"]
-    }
+    "exclude": ["./ignore"]
   }
 }
diff --git a/cli/tests/testdata/test/collect/deno2.jsonc b/cli/tests/testdata/test/collect/deno2.jsonc
index a4d244e31..b7af09d1c 100644
--- a/cli/tests/testdata/test/collect/deno2.jsonc
+++ b/cli/tests/testdata/test/collect/deno2.jsonc
@@ -1,8 +1,6 @@
 {
   "test": {
-    "files": {
-      "include": ["./include/"],
-      "exclude": ["./ignore", "./include/2_test.ts"]
-    }
+    "include": ["./include/"],
+    "exclude": ["./ignore", "./include/2_test.ts"]
   }
 }
diff --git a/cli/tests/testdata/test/collect_with_malformed_config.out b/cli/tests/testdata/test/collect_with_malformed_config.out
index 25c34406f..b31b18e6a 100644
--- a/cli/tests/testdata/test/collect_with_malformed_config.out
+++ b/cli/tests/testdata/test/collect_with_malformed_config.out
@@ -1,4 +1,4 @@
 error: Failed to parse "test" configuration
 
 Caused by:
-    unknown field `dont_know_this_field`, expected `files`
+    unknown field `dont_know_this_field`, expected one of `include`, `exclude`, `files`