Allow arbitrary configuration options to be overridden via the CLI (#9599)

Fixes #8368
Fixes https://github.com/astral-sh/ruff/issues/9186

## Summary

Arbitrary TOML strings can be provided via the command-line to override
configuration options in `pyproject.toml` or `ruff.toml`. As an example:
to run over typeshed and respect typeshed's `pyproject.toml`, but
override a specific isort setting and enable an additional pep8-naming
setting:

```
cargo run -- check ../typeshed --no-cache --config ../typeshed/pyproject.toml --config "lint.isort.combine-as-imports=false" --config "lint.extend-select=['N801']"
```

---------

Co-authored-by: Micha Reiser <micha@reiser.io>
Co-authored-by: Zanie Blue <contact@zanie.dev>

Cargo.lock

@@ -2023,6 +2023,7 @@ dependencies = [
  "test-case",
  "thiserror",
  "tikv-jemallocator",
+ "toml",
  "tracing",
  "walkdir",
  "wild",

crates/ruff/Cargo.toml

@@ -49,6 +49,7 @@ serde_json = { workspace = true }
 shellexpand = { workspace = true }
 strum = { workspace = true, features = [] }
 thiserror = { workspace = true }
+toml = { workspace = true }
 tracing = { workspace = true, features = ["log"] }
 walkdir = { workspace = true }
 wild = { workspace = true }

crates/ruff/src/args.rs

@@ -1,12 +1,18 @@
 use std::cmp::Ordering;
 use std::fmt::Formatter;
-use std::path::PathBuf;
+use std::ops::Deref;
+use std::path::{Path, PathBuf};
 use std::str::FromStr;
+use std::sync::Arc;
 
+use anyhow::bail;
+use clap::builder::{TypedValueParser, ValueParserFactory};
 use clap::{command, Parser};
 use colored::Colorize;
+use path_absolutize::path_dedot;
 use regex::Regex;
 use rustc_hash::FxHashMap;
+use toml;
 
 use ruff_linter::line_width::LineLength;
 use ruff_linter::logging::LogLevel;
@@ -19,7 +25,7 @@ use ruff_linter::{warn_user, RuleParser, RuleSelector, RuleSelectorParser};
 use ruff_source_file::{LineIndex, OneIndexed};
 use ruff_text_size::TextRange;
 use ruff_workspace::configuration::{Configuration, RuleSelection};
-use ruff_workspace::options::PycodestyleOptions;
+use ruff_workspace::options::{Options, PycodestyleOptions};
 use ruff_workspace::resolver::ConfigurationTransformer;
 
 #[derive(Debug, Parser)]
@@ -155,10 +161,20 @@ pub struct CheckCommand {
     preview: bool,
     #[clap(long, overrides_with("preview"), hide = true)]
     no_preview: bool,
-    /// Path to the `pyproject.toml` or `ruff.toml` file to use for
+    /// Either a path to a TOML configuration file (`pyproject.toml` or `ruff.toml`),
-    /// configuration.
+    /// or a TOML `<KEY> = <VALUE>` pair
-    #[arg(long, conflicts_with = "isolated")]
+    /// (such as you might find in a `ruff.toml` configuration file)
-    pub config: Option<PathBuf>,
+    /// overriding a specific configuration option.
+    /// Overrides of individual settings using this option always take precedence
+    /// over all configuration files, including configuration files that were also
+    /// specified using `--config`.
+    #[arg(
+        long,
+        action = clap::ArgAction::Append,
+        value_name = "CONFIG_OPTION",
+        value_parser = ConfigArgumentParser,
+    )]
+    pub config: Vec<SingleConfigArgument>,
     /// Comma-separated list of rule codes to enable (or ALL, to enable all rules).
     #[arg(
         long,
@@ -291,7 +307,15 @@ pub struct CheckCommand {
     #[arg(short, long, env = "RUFF_NO_CACHE", help_heading = "Miscellaneous")]
     pub no_cache: bool,
     /// Ignore all configuration files.
-    #[arg(long, conflicts_with = "config", help_heading = "Miscellaneous")]
+    //
+    // Note: We can't mark this as conflicting with `--config` here
+    // as `--config` can be used for specifying configuration overrides
+    // as well as configuration files.
+    // Specifying a configuration file conflicts with `--isolated`;
+    // specifying a configuration override does not.
+    // If a user specifies `ruff check --isolated --config=ruff.toml`,
+    // we emit an error later on, after the initial parsing by clap.
+    #[arg(long, help_heading = "Miscellaneous")]
     pub isolated: bool,
     /// Path to the cache directory.
     #[arg(long, env = "RUFF_CACHE_DIR", help_heading = "Miscellaneous")]
@@ -384,9 +408,20 @@ pub struct FormatCommand {
     /// difference between the current file and how the formatted file would look like.
     #[arg(long)]
     pub diff: bool,
-    /// Path to the `pyproject.toml` or `ruff.toml` file to use for configuration.
+    /// Either a path to a TOML configuration file (`pyproject.toml` or `ruff.toml`),
-    #[arg(long, conflicts_with = "isolated")]
+    /// or a TOML `<KEY> = <VALUE>` pair
-    pub config: Option<PathBuf>,
+    /// (such as you might find in a `ruff.toml` configuration file)
+    /// overriding a specific configuration option.
+    /// Overrides of individual settings using this option always take precedence
+    /// over all configuration files, including configuration files that were also
+    /// specified using `--config`.
+    #[arg(
+        long,
+        action = clap::ArgAction::Append,
+        value_name = "CONFIG_OPTION",
+        value_parser = ConfigArgumentParser,
+    )]
+    pub config: Vec<SingleConfigArgument>,
 
     /// Disable cache reads.
     #[arg(short, long, env = "RUFF_NO_CACHE", help_heading = "Miscellaneous")]
@@ -428,7 +463,15 @@ pub struct FormatCommand {
     #[arg(long, help_heading = "Format configuration")]
     pub line_length: Option<LineLength>,
     /// Ignore all configuration files.
-    #[arg(long, conflicts_with = "config", help_heading = "Miscellaneous")]
+    //
+    // Note: We can't mark this as conflicting with `--config` here
+    // as `--config` can be used for specifying configuration overrides
+    // as well as configuration files.
+    // Specifying a configuration file conflicts with `--isolated`;
+    // specifying a configuration override does not.
+    // If a user specifies `ruff check --isolated --config=ruff.toml`,
+    // we emit an error later on, after the initial parsing by clap.
+    #[arg(long, help_heading = "Miscellaneous")]
     pub isolated: bool,
     /// The name of the file when passing it through stdin.
     #[arg(long, help_heading = "Miscellaneous")]
@@ -515,101 +558,181 @@ impl From<&LogLevelArgs> for LogLevel {
     }
 }
 
+/// Configuration-related arguments passed via the CLI.
+#[derive(Default)]
+pub struct ConfigArguments {
+    /// Path to a pyproject.toml or ruff.toml configuration file (etc.).
+    /// Either 0 or 1 configuration file paths may be provided on the command line.
+    config_file: Option<PathBuf>,
+    /// Overrides provided via the `--config "KEY=VALUE"` option.
+    /// An arbitrary number of these overrides may be provided on the command line.
+    /// These overrides take precedence over all configuration files,
+    /// even configuration files that were also specified using `--config`.
+    overrides: Configuration,
+    /// Overrides provided via dedicated flags such as `--line-length` etc.
+    /// These overrides take precedence over all configuration files,
+    /// and also over all overrides specified using any `--config "KEY=VALUE"` flags.
+    per_flag_overrides: ExplicitConfigOverrides,
+}
+
+impl ConfigArguments {
+    pub fn config_file(&self) -> Option<&Path> {
+        self.config_file.as_deref()
+    }
+
+    fn from_cli_arguments(
+        config_options: Vec<SingleConfigArgument>,
+        per_flag_overrides: ExplicitConfigOverrides,
+        isolated: bool,
+    ) -> anyhow::Result<Self> {
+        let mut new = Self {
+            per_flag_overrides,
+            ..Self::default()
+        };
+
+        for option in config_options {
+            match option {
+                SingleConfigArgument::SettingsOverride(overridden_option) => {
+                    let overridden_option = Arc::try_unwrap(overridden_option)
+                        .unwrap_or_else(|option| option.deref().clone());
+                    new.overrides = new.overrides.combine(Configuration::from_options(
+                        overridden_option,
+                        None,
+                        &path_dedot::CWD,
+                    )?);
+                }
+                SingleConfigArgument::FilePath(path) => {
+                    if isolated {
+                        bail!(
+                            "\
+The argument `--config={}` cannot be used with `--isolated`
+
+  tip: You cannot specify a configuration file and also specify `--isolated`,
+       as `--isolated` causes ruff to ignore all configuration files.
+       For more information, try `--help`.
+",
+                            path.display()
+                        );
+                    }
+                    if let Some(ref config_file) = new.config_file {
+                        let (first, second) = (config_file.display(), path.display());
+                        bail!(
+                            "\
+You cannot specify more than one configuration file on the command line.
+
+  tip: remove either `--config={first}` or `--config={second}`.
+       For more information, try `--help`.
+"
+                        );
+                    }
+                    new.config_file = Some(path);
+                }
+            }
+        }
+        Ok(new)
+    }
+}
+
+impl ConfigurationTransformer for ConfigArguments {
+    fn transform(&self, config: Configuration) -> Configuration {
+        let with_config_overrides = self.overrides.clone().combine(config);
+        self.per_flag_overrides.transform(with_config_overrides)
+    }
+}
+
 impl CheckCommand {
     /// Partition the CLI into command-line arguments and configuration
     /// overrides.
-    pub fn partition(self) -> (CheckArguments, CliOverrides) {
+    pub fn partition(self) -> anyhow::Result<(CheckArguments, ConfigArguments)> {
-        (
+        let check_arguments = CheckArguments {
-            CheckArguments {
+            add_noqa: self.add_noqa,
-                add_noqa: self.add_noqa,
+            diff: self.diff,
-                config: self.config,
+            ecosystem_ci: self.ecosystem_ci,
-                diff: self.diff,
+            exit_non_zero_on_fix: self.exit_non_zero_on_fix,
-                ecosystem_ci: self.ecosystem_ci,
+            exit_zero: self.exit_zero,
-                exit_non_zero_on_fix: self.exit_non_zero_on_fix,
+            files: self.files,
-                exit_zero: self.exit_zero,
+            ignore_noqa: self.ignore_noqa,
-                files: self.files,
+            isolated: self.isolated,
-                ignore_noqa: self.ignore_noqa,
+            no_cache: self.no_cache,
-                isolated: self.isolated,
+            output_file: self.output_file,
-                no_cache: self.no_cache,
+            show_files: self.show_files,
-                output_file: self.output_file,
+            show_settings: self.show_settings,
-                show_files: self.show_files,
+            statistics: self.statistics,
-                show_settings: self.show_settings,
+            stdin_filename: self.stdin_filename,
-                statistics: self.statistics,
+            watch: self.watch,
-                stdin_filename: self.stdin_filename,
+        };
-                watch: self.watch,
+
-            },
+        let cli_overrides = ExplicitConfigOverrides {
-            CliOverrides {
+            dummy_variable_rgx: self.dummy_variable_rgx,
-                dummy_variable_rgx: self.dummy_variable_rgx,
+            exclude: self.exclude,
-                exclude: self.exclude,
+            extend_exclude: self.extend_exclude,
-                extend_exclude: self.extend_exclude,
+            extend_fixable: self.extend_fixable,
-                extend_fixable: self.extend_fixable,
+            extend_ignore: self.extend_ignore,
-                extend_ignore: self.extend_ignore,
+            extend_per_file_ignores: self.extend_per_file_ignores,
-                extend_per_file_ignores: self.extend_per_file_ignores,
+            extend_select: self.extend_select,
-                extend_select: self.extend_select,
+            extend_unfixable: self.extend_unfixable,
-                extend_unfixable: self.extend_unfixable,
+            fixable: self.fixable,
-                fixable: self.fixable,
+            ignore: self.ignore,
-                ignore: self.ignore,
+            line_length: self.line_length,
-                line_length: self.line_length,
+            per_file_ignores: self.per_file_ignores,
-                per_file_ignores: self.per_file_ignores,
+            preview: resolve_bool_arg(self.preview, self.no_preview).map(PreviewMode::from),
-                preview: resolve_bool_arg(self.preview, self.no_preview).map(PreviewMode::from),
+            respect_gitignore: resolve_bool_arg(self.respect_gitignore, self.no_respect_gitignore),
-                respect_gitignore: resolve_bool_arg(
+            select: self.select,
-                    self.respect_gitignore,
+            target_version: self.target_version,
-                    self.no_respect_gitignore,
+            unfixable: self.unfixable,
-                ),
+            // TODO(charlie): Included in `pyproject.toml`, but not inherited.
-                select: self.select,
+            cache_dir: self.cache_dir,
-                target_version: self.target_version,
+            fix: resolve_bool_arg(self.fix, self.no_fix),
-                unfixable: self.unfixable,
+            fix_only: resolve_bool_arg(self.fix_only, self.no_fix_only),
-                // TODO(charlie): Included in `pyproject.toml`, but not inherited.
+            unsafe_fixes: resolve_bool_arg(self.unsafe_fixes, self.no_unsafe_fixes)
-                cache_dir: self.cache_dir,
+                .map(UnsafeFixes::from),
-                fix: resolve_bool_arg(self.fix, self.no_fix),
+            force_exclude: resolve_bool_arg(self.force_exclude, self.no_force_exclude),
-                fix_only: resolve_bool_arg(self.fix_only, self.no_fix_only),
+            output_format: resolve_output_format(
-                unsafe_fixes: resolve_bool_arg(self.unsafe_fixes, self.no_unsafe_fixes)
+                self.output_format,
-                    .map(UnsafeFixes::from),
+                resolve_bool_arg(self.show_source, self.no_show_source),
-                force_exclude: resolve_bool_arg(self.force_exclude, self.no_force_exclude),
+                resolve_bool_arg(self.preview, self.no_preview).unwrap_or_default(),
-                output_format: resolve_output_format(
+            ),
-                    self.output_format,
+            show_fixes: resolve_bool_arg(self.show_fixes, self.no_show_fixes),
-                    resolve_bool_arg(self.show_source, self.no_show_source),
+            extension: self.extension,
-                    resolve_bool_arg(self.preview, self.no_preview).unwrap_or_default(),
+        };
-                ),
+
-                show_fixes: resolve_bool_arg(self.show_fixes, self.no_show_fixes),
+        let config_args =
-                extension: self.extension,
+            ConfigArguments::from_cli_arguments(self.config, cli_overrides, self.isolated)?;
-            },
+        Ok((check_arguments, config_args))
-        )
     }
 }
 
 impl FormatCommand {
     /// Partition the CLI into command-line arguments and configuration
     /// overrides.
-    pub fn partition(self) -> (FormatArguments, CliOverrides) {
+    pub fn partition(self) -> anyhow::Result<(FormatArguments, ConfigArguments)> {
-        (
+        let format_arguments = FormatArguments {
-            FormatArguments {
+            check: self.check,
-                check: self.check,
+            diff: self.diff,
-                diff: self.diff,
+            files: self.files,
-                config: self.config,
+            isolated: self.isolated,
-                files: self.files,
+            no_cache: self.no_cache,
-                isolated: self.isolated,
+            stdin_filename: self.stdin_filename,
-                no_cache: self.no_cache,
+            range: self.range,
-                stdin_filename: self.stdin_filename,
+        };
-                range: self.range,
-            },
-            CliOverrides {
-                line_length: self.line_length,
-                respect_gitignore: resolve_bool_arg(
-                    self.respect_gitignore,
-                    self.no_respect_gitignore,
-                ),
-                exclude: self.exclude,
-                preview: resolve_bool_arg(self.preview, self.no_preview).map(PreviewMode::from),
-                force_exclude: resolve_bool_arg(self.force_exclude, self.no_force_exclude),
-                target_version: self.target_version,
-                cache_dir: self.cache_dir,
-                extension: self.extension,
 
-                // Unsupported on the formatter CLI, but required on `Overrides`.
+        let cli_overrides = ExplicitConfigOverrides {
-                ..CliOverrides::default()
+            line_length: self.line_length,
-            },
+            respect_gitignore: resolve_bool_arg(self.respect_gitignore, self.no_respect_gitignore),
-        )
+            exclude: self.exclude,
+            preview: resolve_bool_arg(self.preview, self.no_preview).map(PreviewMode::from),
+            force_exclude: resolve_bool_arg(self.force_exclude, self.no_force_exclude),
+            target_version: self.target_version,
+            cache_dir: self.cache_dir,
+            extension: self.extension,
+
+            // Unsupported on the formatter CLI, but required on `Overrides`.
+            ..ExplicitConfigOverrides::default()
+        };
+
+        let config_args =
+            ConfigArguments::from_cli_arguments(self.config, cli_overrides, self.isolated)?;
+        Ok((format_arguments, config_args))
     }
 }
 
@@ -622,6 +745,154 @@ fn resolve_bool_arg(yes: bool, no: bool) -> Option<bool> {
     }
 }
 
+#[derive(Debug)]
+enum TomlParseFailureKind {
+    SyntaxError,
+    UnknownOption,
+}
+
+impl std::fmt::Display for TomlParseFailureKind {
+    fn fmt(&self, f: &mut Formatter<'_>) -> std::fmt::Result {
+        let display = match self {
+            Self::SyntaxError => "The supplied argument is not valid TOML",
+            Self::UnknownOption => {
+                "Could not parse the supplied argument as a `ruff.toml` configuration option"
+            }
+        };
+        write!(f, "{display}")
+    }
+}
+
+#[derive(Debug)]
+struct TomlParseFailure {
+    kind: TomlParseFailureKind,
+    underlying_error: toml::de::Error,
+}
+
+impl std::fmt::Display for TomlParseFailure {
+    fn fmt(&self, f: &mut Formatter<'_>) -> std::fmt::Result {
+        let TomlParseFailure {
+            kind,
+            underlying_error,
+        } = self;
+        let display = format!("{kind}:\n\n{underlying_error}");
+        write!(f, "{}", display.trim_end())
+    }
+}
+
+/// Enumeration to represent a single `--config` argument
+/// passed via the CLI.
+///
+/// Using the `--config` flag, users may pass 0 or 1 paths
+/// to configuration files and an arbitrary number of
+/// "inline TOML" overrides for specific settings.
+///
+/// For example:
+///
+/// ```sh
+/// ruff check --config "path/to/ruff.toml" --config "extend-select=['E501', 'F841']" --config "lint.per-file-ignores = {'some_file.py' = ['F841']}"
+/// ```
+#[derive(Clone, Debug)]
+pub enum SingleConfigArgument {
+    FilePath(PathBuf),
+    SettingsOverride(Arc<Options>),
+}
+
+#[derive(Clone)]
+pub struct ConfigArgumentParser;
+
+impl ValueParserFactory for SingleConfigArgument {
+    type Parser = ConfigArgumentParser;
+
+    fn value_parser() -> Self::Parser {
+        ConfigArgumentParser
+    }
+}
+
+impl TypedValueParser for ConfigArgumentParser {
+    type Value = SingleConfigArgument;
+
+    fn parse_ref(
+        &self,
+        cmd: &clap::Command,
+        arg: Option<&clap::Arg>,
+        value: &std::ffi::OsStr,
+    ) -> Result<Self::Value, clap::Error> {
+        let path_to_config_file = PathBuf::from(value);
+        if path_to_config_file.exists() {
+            return Ok(SingleConfigArgument::FilePath(path_to_config_file));
+        }
+
+        let value = value
+            .to_str()
+            .ok_or_else(|| clap::Error::new(clap::error::ErrorKind::InvalidUtf8))?;
+
+        let toml_parse_error = match toml::Table::from_str(value) {
+            Ok(table) => match table.try_into() {
+                Ok(option) => return Ok(SingleConfigArgument::SettingsOverride(Arc::new(option))),
+                Err(underlying_error) => TomlParseFailure {
+                    kind: TomlParseFailureKind::UnknownOption,
+                    underlying_error,
+                },
+            },
+            Err(underlying_error) => TomlParseFailure {
+                kind: TomlParseFailureKind::SyntaxError,
+                underlying_error,
+            },
+        };
+
+        let mut new_error = clap::Error::new(clap::error::ErrorKind::ValueValidation).with_cmd(cmd);
+        if let Some(arg) = arg {
+            new_error.insert(
+                clap::error::ContextKind::InvalidArg,
+                clap::error::ContextValue::String(arg.to_string()),
+            );
+        }
+        new_error.insert(
+            clap::error::ContextKind::InvalidValue,
+            clap::error::ContextValue::String(value.to_string()),
+        );
+
+        // small hack so that multiline tips
+        // have the same indent on the left-hand side:
+        let tip_indent = " ".repeat("  tip: ".len());
+
+        let mut tip = format!(
+            "\
+A `--config` flag must either be a path to a `.toml` configuration file
+{tip_indent}or a TOML `<KEY> = <VALUE>` pair overriding a specific configuration
+{tip_indent}option"
+        );
+
+        // Here we do some heuristics to try to figure out whether
+        // the user was trying to pass in a path to a configuration file
+        // or some inline TOML.
+        // We want to display the most helpful error to the user as possible.
+        if std::path::Path::new(value)
+            .extension()
+            .map_or(false, |ext| ext.eq_ignore_ascii_case("toml"))
+        {
+            if !value.contains('=') {
+                tip.push_str(&format!(
+                    "
+
+It looks like you were trying to pass a path to a configuration file.
+The path `{value}` does not exist"
+                ));
+            }
+        } else if value.contains('=') {
+            tip.push_str(&format!("\n\n{toml_parse_error}"));
+        }
+
+        new_error.insert(
+            clap::error::ContextKind::Suggested,
+            clap::error::ContextValue::StyledStrs(vec![tip.into()]),
+        );
+
+        Err(new_error)
+    }
+}
+
 fn resolve_output_format(
     output_format: Option<SerializationFormat>,
     show_sources: Option<bool>,
@@ -664,7 +935,6 @@ fn resolve_output_format(
 #[allow(clippy::struct_excessive_bools)]
 pub struct CheckArguments {
     pub add_noqa: bool,
-    pub config: Option<PathBuf>,
     pub diff: bool,
     pub ecosystem_ci: bool,
     pub exit_non_zero_on_fix: bool,
@@ -688,7 +958,6 @@ pub struct FormatArguments {
     pub check: bool,
     pub no_cache: bool,
     pub diff: bool,
-    pub config: Option<PathBuf>,
     pub files: Vec<PathBuf>,
     pub isolated: bool,
     pub stdin_filename: Option<PathBuf>,
@@ -884,39 +1153,40 @@ impl LineColumnParseError {
     }
 }
 
-/// CLI settings that function as configuration overrides.
+/// Configuration overrides provided via dedicated CLI flags:
+/// `--line-length`, `--respect-gitignore`, etc.
 #[derive(Clone, Default)]
 #[allow(clippy::struct_excessive_bools)]
-pub struct CliOverrides {
+struct ExplicitConfigOverrides {
-    pub dummy_variable_rgx: Option<Regex>,
+    dummy_variable_rgx: Option<Regex>,
-    pub exclude: Option<Vec<FilePattern>>,
+    exclude: Option<Vec<FilePattern>>,
-    pub extend_exclude: Option<Vec<FilePattern>>,
+    extend_exclude: Option<Vec<FilePattern>>,
-    pub extend_fixable: Option<Vec<RuleSelector>>,
+    extend_fixable: Option<Vec<RuleSelector>>,
-    pub extend_ignore: Option<Vec<RuleSelector>>,
+    extend_ignore: Option<Vec<RuleSelector>>,
-    pub extend_select: Option<Vec<RuleSelector>>,
+    extend_select: Option<Vec<RuleSelector>>,
-    pub extend_unfixable: Option<Vec<RuleSelector>>,
+    extend_unfixable: Option<Vec<RuleSelector>>,
-    pub fixable: Option<Vec<RuleSelector>>,
+    fixable: Option<Vec<RuleSelector>>,
-    pub ignore: Option<Vec<RuleSelector>>,
+    ignore: Option<Vec<RuleSelector>>,
-    pub line_length: Option<LineLength>,
+    line_length: Option<LineLength>,
-    pub per_file_ignores: Option<Vec<PatternPrefixPair>>,
+    per_file_ignores: Option<Vec<PatternPrefixPair>>,
-    pub extend_per_file_ignores: Option<Vec<PatternPrefixPair>>,
+    extend_per_file_ignores: Option<Vec<PatternPrefixPair>>,
-    pub preview: Option<PreviewMode>,
+    preview: Option<PreviewMode>,
-    pub respect_gitignore: Option<bool>,
+    respect_gitignore: Option<bool>,
-    pub select: Option<Vec<RuleSelector>>,
+    select: Option<Vec<RuleSelector>>,
-    pub target_version: Option<PythonVersion>,
+    target_version: Option<PythonVersion>,
-    pub unfixable: Option<Vec<RuleSelector>>,
+    unfixable: Option<Vec<RuleSelector>>,
     // TODO(charlie): Captured in pyproject.toml as a default, but not part of `Settings`.
-    pub cache_dir: Option<PathBuf>,
+    cache_dir: Option<PathBuf>,
-    pub fix: Option<bool>,
+    fix: Option<bool>,
-    pub fix_only: Option<bool>,
+    fix_only: Option<bool>,
-    pub unsafe_fixes: Option<UnsafeFixes>,
+    unsafe_fixes: Option<UnsafeFixes>,
-    pub force_exclude: Option<bool>,
+    force_exclude: Option<bool>,
-    pub output_format: Option<SerializationFormat>,
+    output_format: Option<SerializationFormat>,
-    pub show_fixes: Option<bool>,
+    show_fixes: Option<bool>,
-    pub extension: Option<Vec<ExtensionPair>>,
+    extension: Option<Vec<ExtensionPair>>,
 }
 
-impl ConfigurationTransformer for CliOverrides {
+impl ConfigurationTransformer for ExplicitConfigOverrides {
     fn transform(&self, mut config: Configuration) -> Configuration {
         if let Some(cache_dir) = &self.cache_dir {
             config.cache_dir = Some(cache_dir.clone());

crates/ruff/src/commands/add_noqa.rs

@@ -12,17 +12,17 @@ use ruff_linter::warn_user_once;
 use ruff_python_ast::{PySourceType, SourceType};
 use ruff_workspace::resolver::{python_files_in_path, PyprojectConfig, ResolvedFile};
 
-use crate::args::CliOverrides;
+use crate::args::ConfigArguments;
 
 /// Add `noqa` directives to a collection of files.
 pub(crate) fn add_noqa(
     files: &[PathBuf],
     pyproject_config: &PyprojectConfig,
-    overrides: &CliOverrides,
+    config_arguments: &ConfigArguments,
 ) -> Result<usize> {
     // Collect all the files to check.
     let start = Instant::now();
-    let (paths, resolver) = python_files_in_path(files, pyproject_config, overrides)?;
+    let (paths, resolver) = python_files_in_path(files, pyproject_config, config_arguments)?;
     let duration = start.elapsed();
     debug!("Identified files to lint in: {:?}", duration);
 

crates/ruff/src/commands/check.rs

@@ -24,7 +24,7 @@ use ruff_workspace::resolver::{
     match_exclusion, python_files_in_path, PyprojectConfig, ResolvedFile,
 };
 
-use crate::args::CliOverrides;
+use crate::args::ConfigArguments;
 use crate::cache::{Cache, PackageCacheMap, PackageCaches};
 use crate::diagnostics::Diagnostics;
 use crate::panic::catch_unwind;
@@ -34,7 +34,7 @@ use crate::panic::catch_unwind;
 pub(crate) fn check(
     files: &[PathBuf],
     pyproject_config: &PyprojectConfig,
-    overrides: &CliOverrides,
+    config_arguments: &ConfigArguments,
     cache: flags::Cache,
     noqa: flags::Noqa,
     fix_mode: flags::FixMode,
@@ -42,7 +42,7 @@ pub(crate) fn check(
 ) -> Result<Diagnostics> {
     // Collect all the Python files to check.
     let start = Instant::now();
-    let (paths, resolver) = python_files_in_path(files, pyproject_config, overrides)?;
+    let (paths, resolver) = python_files_in_path(files, pyproject_config, config_arguments)?;
     debug!("Identified files to lint in: {:?}", start.elapsed());
 
     if paths.is_empty() {
@@ -233,7 +233,7 @@ mod test {
     use ruff_workspace::resolver::{PyprojectConfig, PyprojectDiscoveryStrategy};
     use ruff_workspace::Settings;
 
-    use crate::args::CliOverrides;
+    use crate::args::ConfigArguments;
 
     use super::check;
 
@@ -272,7 +272,7 @@ mod test {
             // Notebooks are not included by default
             &[tempdir.path().to_path_buf(), notebook],
             &pyproject_config,
-            &CliOverrides::default(),
+            &ConfigArguments::default(),
             flags::Cache::Disabled,
             flags::Noqa::Disabled,
             flags::FixMode::Generate,

crates/ruff/src/commands/check_stdin.rs

@@ -6,7 +6,7 @@ use ruff_linter::packaging;
 use ruff_linter::settings::flags;
 use ruff_workspace::resolver::{match_exclusion, python_file_at_path, PyprojectConfig, Resolver};
 
-use crate::args::CliOverrides;
+use crate::args::ConfigArguments;
 use crate::diagnostics::{lint_stdin, Diagnostics};
 use crate::stdin::{parrot_stdin, read_from_stdin};
 
@@ -14,7 +14,7 @@ use crate::stdin::{parrot_stdin, read_from_stdin};
 pub(crate) fn check_stdin(
     filename: Option<&Path>,
     pyproject_config: &PyprojectConfig,
-    overrides: &CliOverrides,
+    overrides: &ConfigArguments,
     noqa: flags::Noqa,
     fix_mode: flags::FixMode,
 ) -> Result<Diagnostics> {

crates/ruff/src/commands/format.rs

@@ -29,7 +29,7 @@ use ruff_text_size::{TextLen, TextRange, TextSize};
 use ruff_workspace::resolver::{match_exclusion, python_files_in_path, ResolvedFile, Resolver};
 use ruff_workspace::FormatterSettings;
 
-use crate::args::{CliOverrides, FormatArguments, FormatRange};
+use crate::args::{ConfigArguments, FormatArguments, FormatRange};
 use crate::cache::{Cache, FileCacheKey, PackageCacheMap, PackageCaches};
 use crate::panic::{catch_unwind, PanicError};
 use crate::resolve::resolve;
@@ -60,18 +60,17 @@ impl FormatMode {
 /// Format a set of files, and return the exit status.
 pub(crate) fn format(
     cli: FormatArguments,
-    overrides: &CliOverrides,
+    config_arguments: &ConfigArguments,
     log_level: LogLevel,
 ) -> Result<ExitStatus> {
     let pyproject_config = resolve(
         cli.isolated,
-        cli.config.as_deref(),
+        config_arguments,
-        overrides,
         cli.stdin_filename.as_deref(),
     )?;
     let mode = FormatMode::from_cli(&cli);
     let files = resolve_default_files(cli.files, false);
-    let (paths, resolver) = python_files_in_path(&files, &pyproject_config, overrides)?;
+    let (paths, resolver) = python_files_in_path(&files, &pyproject_config, config_arguments)?;
 
     if paths.is_empty() {
         warn_user_once!("No Python files found under the given path(s)");

crates/ruff/src/commands/format_stdin.rs

@@ -9,7 +9,7 @@ use ruff_python_ast::{PySourceType, SourceType};
 use ruff_workspace::resolver::{match_exclusion, python_file_at_path, Resolver};
 use ruff_workspace::FormatterSettings;
 
-use crate::args::{CliOverrides, FormatArguments, FormatRange};
+use crate::args::{ConfigArguments, FormatArguments, FormatRange};
 use crate::commands::format::{
     format_source, warn_incompatible_formatter_settings, FormatCommandError, FormatMode,
     FormatResult, FormattedSource,
@@ -19,11 +19,13 @@ use crate::stdin::{parrot_stdin, read_from_stdin};
 use crate::ExitStatus;
 
 /// Run the formatter over a single file, read from `stdin`.
-pub(crate) fn format_stdin(cli: &FormatArguments, overrides: &CliOverrides) -> Result<ExitStatus> {
+pub(crate) fn format_stdin(
+    cli: &FormatArguments,
+    config_arguments: &ConfigArguments,
+) -> Result<ExitStatus> {
     let pyproject_config = resolve(
         cli.isolated,
-        cli.config.as_deref(),
+        config_arguments,
-        overrides,
         cli.stdin_filename.as_deref(),
     )?;
 
@@ -34,7 +36,7 @@ pub(crate) fn format_stdin(cli: &FormatArguments, overrides: &CliOverrides) -> R
 
     if resolver.force_exclude() {
         if let Some(filename) = cli.stdin_filename.as_deref() {
-            if !python_file_at_path(filename, &mut resolver, overrides)? {
+            if !python_file_at_path(filename, &mut resolver, config_arguments)? {
                 if mode.is_write() {
                     parrot_stdin()?;
                 }

crates/ruff/src/commands/show_files.rs

@@ -7,17 +7,17 @@ use itertools::Itertools;
 use ruff_linter::warn_user_once;
 use ruff_workspace::resolver::{python_files_in_path, PyprojectConfig, ResolvedFile};
 
-use crate::args::CliOverrides;
+use crate::args::ConfigArguments;
 
 /// Show the list of files to be checked based on current settings.
 pub(crate) fn show_files(
     files: &[PathBuf],
     pyproject_config: &PyprojectConfig,
-    overrides: &CliOverrides,
+    config_arguments: &ConfigArguments,
     writer: &mut impl Write,
 ) -> Result<()> {
     // Collect all files in the hierarchy.
-    let (paths, _resolver) = python_files_in_path(files, pyproject_config, overrides)?;
+    let (paths, _resolver) = python_files_in_path(files, pyproject_config, config_arguments)?;
 
     if paths.is_empty() {
         warn_user_once!("No Python files found under the given path(s)");

crates/ruff/src/commands/show_settings.rs

@@ -6,17 +6,17 @@ use itertools::Itertools;
 
 use ruff_workspace::resolver::{python_files_in_path, PyprojectConfig, ResolvedFile};
 
-use crate::args::CliOverrides;
+use crate::args::ConfigArguments;
 
 /// Print the user-facing configuration settings.
 pub(crate) fn show_settings(
     files: &[PathBuf],
     pyproject_config: &PyprojectConfig,
-    overrides: &CliOverrides,
+    config_arguments: &ConfigArguments,
     writer: &mut impl Write,
 ) -> Result<()> {
     // Collect all files in the hierarchy.
-    let (paths, resolver) = python_files_in_path(files, pyproject_config, overrides)?;
+    let (paths, resolver) = python_files_in_path(files, pyproject_config, config_arguments)?;
 
     // Print the list of files.
     let Some(path) = paths

crates/ruff/src/lib.rs

@@ -204,24 +204,23 @@ pub fn run(
 }
 
 fn format(args: FormatCommand, log_level: LogLevel) -> Result<ExitStatus> {
-    let (cli, overrides) = args.partition();
+    let (cli, config_arguments) = args.partition()?;
 
     if is_stdin(&cli.files, cli.stdin_filename.as_deref()) {
-        commands::format_stdin::format_stdin(&cli, &overrides)
+        commands::format_stdin::format_stdin(&cli, &config_arguments)
     } else {
-        commands::format::format(cli, &overrides, log_level)
+        commands::format::format(cli, &config_arguments, log_level)
     }
 }
 
 pub fn check(args: CheckCommand, log_level: LogLevel) -> Result<ExitStatus> {
-    let (cli, overrides) = args.partition();
+    let (cli, config_arguments) = args.partition()?;
 
     // Construct the "default" settings. These are used when no `pyproject.toml`
     // files are present, or files are injected from outside of the hierarchy.
     let pyproject_config = resolve::resolve(
         cli.isolated,
-        cli.config.as_deref(),
+        &config_arguments,
-        &overrides,
         cli.stdin_filename.as_deref(),
     )?;
 
@@ -239,11 +238,21 @@ pub fn check(args: CheckCommand, log_level: LogLevel) -> Result<ExitStatus> {
     let files = resolve_default_files(cli.files, is_stdin);
 
     if cli.show_settings {
-        commands::show_settings::show_settings(&files, &pyproject_config, &overrides, &mut writer)?;
+        commands::show_settings::show_settings(
+            &files,
+            &pyproject_config,
+            &config_arguments,
+            &mut writer,
+        )?;
         return Ok(ExitStatus::Success);
     }
     if cli.show_files {
-        commands::show_files::show_files(&files, &pyproject_config, &overrides, &mut writer)?;
+        commands::show_files::show_files(
+            &files,
+            &pyproject_config,
+            &config_arguments,
+            &mut writer,
+        )?;
         return Ok(ExitStatus::Success);
     }
 
@@ -302,7 +311,8 @@ pub fn check(args: CheckCommand, log_level: LogLevel) -> Result<ExitStatus> {
         if !fix_mode.is_generate() {
             warn_user!("--fix is incompatible with --add-noqa.");
         }
-        let modifications = commands::add_noqa::add_noqa(&files, &pyproject_config, &overrides)?;
+        let modifications =
+            commands::add_noqa::add_noqa(&files, &pyproject_config, &config_arguments)?;
         if modifications > 0 && log_level >= LogLevel::Default {
             let s = if modifications == 1 { "" } else { "s" };
             #[allow(clippy::print_stderr)]
@@ -352,7 +362,7 @@ pub fn check(args: CheckCommand, log_level: LogLevel) -> Result<ExitStatus> {
         let messages = commands::check::check(
             &files,
             &pyproject_config,
-            &overrides,
+            &config_arguments,
             cache.into(),
             noqa.into(),
             fix_mode,
@@ -374,8 +384,7 @@ pub fn check(args: CheckCommand, log_level: LogLevel) -> Result<ExitStatus> {
                     if matches!(change_kind, ChangeKind::Configuration) {
                         pyproject_config = resolve::resolve(
                             cli.isolated,
-                            cli.config.as_deref(),
+                            &config_arguments,
-                            &overrides,
                             cli.stdin_filename.as_deref(),
                         )?;
                     }
@@ -385,7 +394,7 @@ pub fn check(args: CheckCommand, log_level: LogLevel) -> Result<ExitStatus> {
                     let messages = commands::check::check(
                         &files,
                         &pyproject_config,
-                        &overrides,
+                        &config_arguments,
                         cache.into(),
                         noqa.into(),
                         fix_mode,
@@ -402,7 +411,7 @@ pub fn check(args: CheckCommand, log_level: LogLevel) -> Result<ExitStatus> {
             commands::check_stdin::check_stdin(
                 cli.stdin_filename.map(fs::normalize_path).as_deref(),
                 &pyproject_config,
-                &overrides,
+                &config_arguments,
                 noqa.into(),
                 fix_mode,
             )?
@@ -410,7 +419,7 @@ pub fn check(args: CheckCommand, log_level: LogLevel) -> Result<ExitStatus> {
             commands::check::check(
                 &files,
                 &pyproject_config,
-                &overrides,
+                &config_arguments,
                 cache.into(),
                 noqa.into(),
                 fix_mode,

crates/ruff/src/resolve.rs

@@ -11,19 +11,18 @@ use ruff_workspace::resolver::{
     Relativity,
 };
 
-use crate::args::CliOverrides;
+use crate::args::ConfigArguments;
 
 /// Resolve the relevant settings strategy and defaults for the current
 /// invocation.
 pub fn resolve(
     isolated: bool,
-    config: Option<&Path>,
+    config_arguments: &ConfigArguments,
-    overrides: &CliOverrides,
     stdin_filename: Option<&Path>,
 ) -> Result<PyprojectConfig> {
     // First priority: if we're running in isolated mode, use the default settings.
     if isolated {
-        let config = overrides.transform(Configuration::default());
+        let config = config_arguments.transform(Configuration::default());
         let settings = config.into_settings(&path_dedot::CWD)?;
         debug!("Isolated mode, not reading any pyproject.toml");
         return Ok(PyprojectConfig::new(
@@ -36,12 +35,13 @@ pub fn resolve(
     // Second priority: the user specified a `pyproject.toml` file. Use that
     // `pyproject.toml` for _all_ configuration, and resolve paths relative to the
     // current working directory. (This matches ESLint's behavior.)
-    if let Some(pyproject) = config
+    if let Some(pyproject) = config_arguments
+        .config_file()
         .map(|config| config.display().to_string())
         .map(|config| shellexpand::full(&config).map(|config| PathBuf::from(config.as_ref())))
         .transpose()?
     {
-        let settings = resolve_root_settings(&pyproject, Relativity::Cwd, overrides)?;
+        let settings = resolve_root_settings(&pyproject, Relativity::Cwd, config_arguments)?;
         debug!(
             "Using user-specified configuration file at: {}",
             pyproject.display()
@@ -67,7 +67,7 @@ pub fn resolve(
             "Using configuration file (via parent) at: {}",
             pyproject.display()
         );
-        let settings = resolve_root_settings(&pyproject, Relativity::Parent, overrides)?;
+        let settings = resolve_root_settings(&pyproject, Relativity::Parent, config_arguments)?;
         return Ok(PyprojectConfig::new(
             PyprojectDiscoveryStrategy::Hierarchical,
             settings,
@@ -84,7 +84,7 @@ pub fn resolve(
             "Using configuration file (via cwd) at: {}",
             pyproject.display()
         );
-        let settings = resolve_root_settings(&pyproject, Relativity::Cwd, overrides)?;
+        let settings = resolve_root_settings(&pyproject, Relativity::Cwd, config_arguments)?;
         return Ok(PyprojectConfig::new(
             PyprojectDiscoveryStrategy::Hierarchical,
             settings,
@@ -97,7 +97,7 @@ pub fn resolve(
     // "closest" `pyproject.toml` file for every Python file later on, so these act
     // as the "default" settings.)
     debug!("Using Ruff default settings");
-    let config = overrides.transform(Configuration::default());
+    let config = config_arguments.transform(Configuration::default());
     let settings = config.into_settings(&path_dedot::CWD)?;
     Ok(PyprojectConfig::new(
         PyprojectDiscoveryStrategy::Hierarchical,

crates/ruff/tests/format.rs

@@ -90,6 +90,179 @@ fn format_warn_stdin_filename_with_files() {
     "###);
 }
 
+#[test]
+fn nonexistent_config_file() {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(["format", "--config", "foo.toml", "."]), @r###"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    error: invalid value 'foo.toml' for '--config <CONFIG_OPTION>'
+
+      tip: A `--config` flag must either be a path to a `.toml` configuration file
+           or a TOML `<KEY> = <VALUE>` pair overriding a specific configuration
+           option
+
+    It looks like you were trying to pass a path to a configuration file.
+    The path `foo.toml` does not exist
+
+    For more information, try '--help'.
+    "###);
+}
+
+#[test]
+fn config_override_rejected_if_invalid_toml() {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(["format", "--config", "foo = bar", "."]), @r###"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    error: invalid value 'foo = bar' for '--config <CONFIG_OPTION>'
+
+      tip: A `--config` flag must either be a path to a `.toml` configuration file
+           or a TOML `<KEY> = <VALUE>` pair overriding a specific configuration
+           option
+
+    The supplied argument is not valid TOML:
+
+    TOML parse error at line 1, column 7
+      |
+    1 | foo = bar
+      |       ^
+    invalid string
+    expected `"`, `'`
+
+    For more information, try '--help'.
+    "###);
+}
+
+#[test]
+fn too_many_config_files() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_dot_toml = tempdir.path().join("ruff.toml");
+    let ruff2_dot_toml = tempdir.path().join("ruff2.toml");
+    fs::File::create(&ruff_dot_toml)?;
+    fs::File::create(&ruff2_dot_toml)?;
+    let expected_stderr = format!(
+        "\
+ruff failed
+  Cause: You cannot specify more than one configuration file on the command line.
+
+  tip: remove either `--config={}` or `--config={}`.
+       For more information, try `--help`.
+
+",
+        ruff_dot_toml.display(),
+        ruff2_dot_toml.display(),
+    );
+    let cmd = Command::new(get_cargo_bin(BIN_NAME))
+        .arg("format")
+        .arg("--config")
+        .arg(&ruff_dot_toml)
+        .arg("--config")
+        .arg(&ruff2_dot_toml)
+        .arg(".")
+        .output()?;
+    let stderr = std::str::from_utf8(&cmd.stderr)?;
+    assert_eq!(stderr, expected_stderr);
+    Ok(())
+}
+
+#[test]
+fn config_file_and_isolated() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_dot_toml = tempdir.path().join("ruff.toml");
+    fs::File::create(&ruff_dot_toml)?;
+    let expected_stderr = format!(
+        "\
+ruff failed
+  Cause: The argument `--config={}` cannot be used with `--isolated`
+
+  tip: You cannot specify a configuration file and also specify `--isolated`,
+       as `--isolated` causes ruff to ignore all configuration files.
+       For more information, try `--help`.
+
+",
+        ruff_dot_toml.display(),
+    );
+    let cmd = Command::new(get_cargo_bin(BIN_NAME))
+        .arg("format")
+        .arg("--config")
+        .arg(&ruff_dot_toml)
+        .arg("--isolated")
+        .arg(".")
+        .output()?;
+    let stderr = std::str::from_utf8(&cmd.stderr)?;
+    assert_eq!(stderr, expected_stderr);
+    Ok(())
+}
+
+#[test]
+fn config_override_via_cli() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_toml = tempdir.path().join("ruff.toml");
+    fs::write(&ruff_toml, "line-length = 100")?;
+    let fixture = r#"
+def foo():
+    print("looooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooong string")
+
+    "#;
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .arg("format")
+        .arg("--config")
+        .arg(&ruff_toml)
+        // This overrides the long line length set in the config file
+        .args(["--config", "line-length=80"])
+        .arg("-")
+        .pass_stdin(fixture), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+    def foo():
+        print(
+            "looooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooong string"
+        )
+
+    ----- stderr -----
+    "###);
+    Ok(())
+}
+
+#[test]
+fn config_doubly_overridden_via_cli() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_toml = tempdir.path().join("ruff.toml");
+    fs::write(&ruff_toml, "line-length = 70")?;
+    let fixture = r#"
+def foo():
+    print("looooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooong string")
+
+    "#;
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .arg("format")
+        .arg("--config")
+        .arg(&ruff_toml)
+        // This overrides the long line length set in the config file...
+        .args(["--config", "line-length=80"])
+        // ...but this overrides them both:
+        .args(["--line-length", "100"])
+        .arg("-")
+        .pass_stdin(fixture), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+    def foo():
+        print("looooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooong string")
+
+    ----- stderr -----
+    "###);
+    Ok(())
+}
+
 #[test]
 fn format_options() -> Result<()> {
     let tempdir = TempDir::new()?;

crates/ruff/tests/lint.rs

@@ -510,6 +510,341 @@ ignore = ["D203", "D212"]
     Ok(())
 }
 
+#[test]
+fn nonexistent_config_file() {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        .args(["--config", "foo.toml", "."]), @r###"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    error: invalid value 'foo.toml' for '--config <CONFIG_OPTION>'
+
+      tip: A `--config` flag must either be a path to a `.toml` configuration file
+           or a TOML `<KEY> = <VALUE>` pair overriding a specific configuration
+           option
+
+    It looks like you were trying to pass a path to a configuration file.
+    The path `foo.toml` does not exist
+
+    For more information, try '--help'.
+    "###);
+}
+
+#[test]
+fn config_override_rejected_if_invalid_toml() {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        .args(["--config", "foo = bar", "."]), @r###"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    error: invalid value 'foo = bar' for '--config <CONFIG_OPTION>'
+
+      tip: A `--config` flag must either be a path to a `.toml` configuration file
+           or a TOML `<KEY> = <VALUE>` pair overriding a specific configuration
+           option
+
+    The supplied argument is not valid TOML:
+
+    TOML parse error at line 1, column 7
+      |
+    1 | foo = bar
+      |       ^
+    invalid string
+    expected `"`, `'`
+
+    For more information, try '--help'.
+    "###);
+}
+
+#[test]
+fn too_many_config_files() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_dot_toml = tempdir.path().join("ruff.toml");
+    let ruff2_dot_toml = tempdir.path().join("ruff2.toml");
+    fs::File::create(&ruff_dot_toml)?;
+    fs::File::create(&ruff2_dot_toml)?;
+    insta::with_settings!({
+        filters => vec![(tempdir_filter(&tempdir).as_str(), "[TMP]/")]
+    }, {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        .arg("--config")
+        .arg(&ruff_dot_toml)
+        .arg("--config")
+        .arg(&ruff2_dot_toml)
+        .arg("."), @r###"
+        success: false
+        exit_code: 2
+        ----- stdout -----
+
+        ----- stderr -----
+        ruff failed
+          Cause: You cannot specify more than one configuration file on the command line.
+
+          tip: remove either `--config=[TMP]/ruff.toml` or `--config=[TMP]/ruff2.toml`.
+               For more information, try `--help`.
+
+        "###);
+    });
+    Ok(())
+}
+
+#[test]
+fn config_file_and_isolated() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_dot_toml = tempdir.path().join("ruff.toml");
+    fs::File::create(&ruff_dot_toml)?;
+    insta::with_settings!({
+        filters => vec![(tempdir_filter(&tempdir).as_str(), "[TMP]/")]
+    }, {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        .arg("--config")
+        .arg(&ruff_dot_toml)
+        .arg("--isolated")
+        .arg("."), @r###"
+        success: false
+        exit_code: 2
+        ----- stdout -----
+
+        ----- stderr -----
+        ruff failed
+          Cause: The argument `--config=[TMP]/ruff.toml` cannot be used with `--isolated`
+
+          tip: You cannot specify a configuration file and also specify `--isolated`,
+               as `--isolated` causes ruff to ignore all configuration files.
+               For more information, try `--help`.
+
+        "###);
+    });
+    Ok(())
+}
+
+#[test]
+fn config_override_via_cli() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_toml = tempdir.path().join("ruff.toml");
+    fs::write(
+        &ruff_toml,
+        r#"
+line-length = 100
+
+[lint]
+select = ["I"]
+
+[lint.isort]
+combine-as-imports = true
+        "#,
+    )?;
+    let fixture = r#"
+from foo import (
+    aaaaaaaaaaaaaaaaaaa,
+    bbbbbbbbbbb as bbbbbbbbbbbbbbbb,
+    cccccccccccccccc,
+    ddddddddddd as ddddddddddddd,
+    eeeeeeeeeeeeeee,
+    ffffffffffff as ffffffffffffff,
+    ggggggggggggg,
+    hhhhhhh as hhhhhhhhhhh,
+    iiiiiiiiiiiiii,
+    jjjjjjjjjjjjj as jjjjjj,
+)
+
+x = "longer_than_90_charactersssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss"
+"#;
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        .arg("--config")
+        .arg(&ruff_toml)
+        .args(["--config", "line-length=90"])
+        .args(["--config", "lint.extend-select=['E501', 'F841']"])
+        .args(["--config", "lint.isort.combine-as-imports = false"])
+        .arg("-")
+        .pass_stdin(fixture), @r###"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    -:2:1: I001 [*] Import block is un-sorted or un-formatted
+    -:15:91: E501 Line too long (97 > 90)
+    Found 2 errors.
+    [*] 1 fixable with the `--fix` option.
+
+    ----- stderr -----
+    "###);
+    Ok(())
+}
+
+#[test]
+fn valid_toml_but_nonexistent_option_provided_via_config_argument() {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        .args([".", "--config", "extend-select=['F481']"]),  // No such code as F481!
+        @r###"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    error: invalid value 'extend-select=['F481']' for '--config <CONFIG_OPTION>'
+
+      tip: A `--config` flag must either be a path to a `.toml` configuration file
+           or a TOML `<KEY> = <VALUE>` pair overriding a specific configuration
+           option
+
+    Could not parse the supplied argument as a `ruff.toml` configuration option:
+
+    Unknown rule selector: `F481`
+
+    For more information, try '--help'.
+    "###);
+}
+
+#[test]
+fn each_toml_option_requires_a_new_flag_1() {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        // commas can't be used to delimit different config overrides;
+        // you need a new --config flag for each override
+        .args([".", "--config", "extend-select=['F841'], line-length=90"]),
+        @r###"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    error: invalid value 'extend-select=['F841'], line-length=90' for '--config <CONFIG_OPTION>'
+
+      tip: A `--config` flag must either be a path to a `.toml` configuration file
+           or a TOML `<KEY> = <VALUE>` pair overriding a specific configuration
+           option
+
+    The supplied argument is not valid TOML:
+
+    TOML parse error at line 1, column 23
+      |
+    1 | extend-select=['F841'], line-length=90
+      |                       ^
+    expected newline, `#`
+
+    For more information, try '--help'.
+    "###);
+}
+
+#[test]
+fn each_toml_option_requires_a_new_flag_2() {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        // spaces *also* can't be used to delimit different config overrides;
+        // you need a new --config flag for each override
+        .args([".", "--config", "extend-select=['F841'] line-length=90"]),
+        @r###"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    error: invalid value 'extend-select=['F841'] line-length=90' for '--config <CONFIG_OPTION>'
+
+      tip: A `--config` flag must either be a path to a `.toml` configuration file
+           or a TOML `<KEY> = <VALUE>` pair overriding a specific configuration
+           option
+
+    The supplied argument is not valid TOML:
+
+    TOML parse error at line 1, column 24
+      |
+    1 | extend-select=['F841'] line-length=90
+      |                        ^
+    expected newline, `#`
+
+    For more information, try '--help'.
+    "###);
+}
+
+#[test]
+fn config_doubly_overridden_via_cli() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_toml = tempdir.path().join("ruff.toml");
+    fs::write(
+        &ruff_toml,
+        r#"
+line-length = 100
+
+[lint]
+select=["E501"]
+"#,
+    )?;
+    let fixture = "x = 'longer_than_90_charactersssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss'";
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        // The --line-length flag takes priority over both the config file
+        // and the `--config="line-length=110"` flag,
+        // despite them both being specified after this flag on the command line:
+        .args(["--line-length", "90"])
+        .arg("--config")
+        .arg(&ruff_toml)
+        .args(["--config", "line-length=110"])
+        .arg("-")
+        .pass_stdin(fixture), @r###"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    -:1:91: E501 Line too long (97 > 90)
+    Found 1 error.
+
+    ----- stderr -----
+    "###);
+    Ok(())
+}
+
+#[test]
+fn complex_config_setting_overridden_via_cli() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let ruff_toml = tempdir.path().join("ruff.toml");
+    fs::write(&ruff_toml, "lint.select = ['N801']")?;
+    let fixture = "class violates_n801: pass";
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        .arg("--config")
+        .arg(&ruff_toml)
+        .args(["--config", "lint.per-file-ignores = {'generated.py' = ['N801']}"])
+        .args(["--stdin-filename", "generated.py"])
+        .arg("-")
+        .pass_stdin(fixture), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    "###);
+    Ok(())
+}
+
+#[test]
+fn deprecated_config_option_overridden_via_cli() {
+    assert_cmd_snapshot!(Command::new(get_cargo_bin(BIN_NAME))
+        .args(STDIN_BASE_OPTIONS)
+        .args(["--config", "select=['N801']", "-"])
+        .pass_stdin("class lowercase: ..."),
+        @r###"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    -:1:7: N801 Class name `lowercase` should use CapWords convention 
+    Found 1 error.
+
+    ----- stderr -----
+    warning: The top-level linter settings are deprecated in favour of their counterparts in the `lint` section. Please update the following options in your `--config` CLI arguments:
+      - 'select' -> 'lint.select'
+    "###);
+}
+
 #[test]
 fn extension() -> Result<()> {
     let tempdir = TempDir::new()?;

crates/ruff_dev/src/format_dev.rs

@@ -27,7 +27,7 @@ use tracing_subscriber::layer::SubscriberExt;
 use tracing_subscriber::util::SubscriberInitExt;
 use tracing_subscriber::EnvFilter;
 
-use ruff::args::{CliOverrides, FormatArguments, FormatCommand, LogLevelArgs};
+use ruff::args::{ConfigArguments, FormatArguments, FormatCommand, LogLevelArgs};
 use ruff::resolve::resolve;
 use ruff_formatter::{FormatError, LineWidth, PrintError};
 use ruff_linter::logging::LogLevel;
@@ -38,24 +38,23 @@ use ruff_python_formatter::{
 use ruff_python_parser::ParseError;
 use ruff_workspace::resolver::{python_files_in_path, PyprojectConfig, ResolvedFile, Resolver};
 
-fn parse_cli(dirs: &[PathBuf]) -> anyhow::Result<(FormatArguments, CliOverrides)> {
+fn parse_cli(dirs: &[PathBuf]) -> anyhow::Result<(FormatArguments, ConfigArguments)> {
     let args_matches = FormatCommand::command()
         .no_binary_name(true)
         .get_matches_from(dirs);
     let arguments: FormatCommand = FormatCommand::from_arg_matches(&args_matches)?;
-    let (cli, overrides) = arguments.partition();
+    let (cli, config_arguments) = arguments.partition()?;
-    Ok((cli, overrides))
+    Ok((cli, config_arguments))
 }
 
 /// Find the [`PyprojectConfig`] to use for formatting.
 fn find_pyproject_config(
     cli: &FormatArguments,
-    overrides: &CliOverrides,
+    config_arguments: &ConfigArguments,
 ) -> anyhow::Result<PyprojectConfig> {
     let mut pyproject_config = resolve(
         cli.isolated,
-        cli.config.as_deref(),
+        config_arguments,
-        overrides,
         cli.stdin_filename.as_deref(),
     )?;
     // We don't want to format pyproject.toml
@@ -72,9 +71,9 @@ fn find_pyproject_config(
 fn ruff_check_paths<'a>(
     pyproject_config: &'a PyprojectConfig,
     cli: &FormatArguments,
-    overrides: &CliOverrides,
+    config_arguments: &ConfigArguments,
 ) -> anyhow::Result<(Vec<Result<ResolvedFile, ignore::Error>>, Resolver<'a>)> {
-    let (paths, resolver) = python_files_in_path(&cli.files, pyproject_config, overrides)?;
+    let (paths, resolver) = python_files_in_path(&cli.files, pyproject_config, config_arguments)?;
     Ok((paths, resolver))
 }
 

crates/ruff_linter/src/settings/types.rs

@@ -534,7 +534,7 @@ impl SerializationFormat {
     }
 }
 
-#[derive(Debug, PartialEq, Eq, Serialize, Deserialize, Hash)]
+#[derive(Clone, Debug, PartialEq, Eq, Serialize, Deserialize, Hash)]
 #[serde(try_from = "String")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
 pub struct Version(String);

crates/ruff_wasm/src/lib.rs

@@ -108,8 +108,9 @@ impl Workspace {
     #[wasm_bindgen(constructor)]
     pub fn new(options: JsValue) -> Result<Workspace, Error> {
         let options: Options = serde_wasm_bindgen::from_value(options).map_err(into_error)?;
-        let configuration = Configuration::from_options(options, Path::new("."), Path::new("."))
+        let configuration =
-            .map_err(into_error)?;
+            Configuration::from_options(options, Some(Path::new(".")), Path::new("."))
+                .map_err(into_error)?;
         let settings = configuration
             .into_settings(Path::new("."))
             .map_err(into_error)?;

crates/ruff_workspace/src/configuration.rs

@@ -51,7 +51,7 @@ use crate::settings::{
     FileResolverSettings, FormatterSettings, LineEnding, Settings, EXCLUDE, INCLUDE,
 };
 
-#[derive(Debug, Default)]
+#[derive(Clone, Debug, Default)]
 pub struct RuleSelection {
     pub select: Option<Vec<RuleSelector>>,
     pub ignore: Vec<RuleSelector>,
@@ -106,7 +106,7 @@ impl RuleSelection {
     }
 }
 
-#[derive(Debug, Default)]
+#[derive(Debug, Default, Clone)]
 pub struct Configuration {
     // Global options
     pub cache_dir: Option<PathBuf>,
@@ -397,7 +397,13 @@ impl Configuration {
     }
 
     /// Convert the [`Options`] read from the given [`Path`] into a [`Configuration`].
-    pub fn from_options(options: Options, path: &Path, project_root: &Path) -> Result<Self> {
+    /// If `None` is supplied for `path`, it indicates that the `Options` instance
+    /// was created via "inline TOML" from the `--config` flag
+    pub fn from_options(
+        options: Options,
+        path: Option<&Path>,
+        project_root: &Path,
+    ) -> Result<Self> {
         warn_about_deprecated_top_level_lint_options(&options.lint_top_level.0, path);
 
         let lint = if let Some(mut lint) = options.lint {
@@ -578,7 +584,7 @@ impl Configuration {
     }
 }
 
-#[derive(Debug, Default)]
+#[derive(Clone, Debug, Default)]
 pub struct LintConfiguration {
     pub exclude: Option<Vec<FilePattern>>,
     pub preview: Option<PreviewMode>,
@@ -1155,7 +1161,7 @@ impl LintConfiguration {
     }
 }
 
-#[derive(Debug, Default)]
+#[derive(Clone, Debug, Default)]
 pub struct FormatConfiguration {
     pub exclude: Option<Vec<FilePattern>>,
     pub preview: Option<PreviewMode>,
@@ -1263,7 +1269,7 @@ pub fn resolve_src(src: &[String], project_root: &Path) -> Result<Vec<PathBuf>>
 
 fn warn_about_deprecated_top_level_lint_options(
     top_level_options: &LintCommonOptions,
-    path: &Path,
+    path: Option<&Path>,
 ) {
     let mut used_options = Vec::new();
 
@@ -1454,9 +1460,14 @@ fn warn_about_deprecated_top_level_lint_options(
         .map(|option| format!("- '{option}' -> 'lint.{option}'"))
         .join("\n  ");
 
+    let thing_to_update = path.map_or_else(
+        || String::from("your `--config` CLI arguments"),
+        |path| format!("`{}`", fs::relativize_path(path)),
+    );
+
     warn_user_once_by_message!(
-        "The top-level linter settings are deprecated in favour of their counterparts in the `lint` section. Please update the following options in `{}`:\n  {options_mapping}",
+        "The top-level linter settings are deprecated in favour of their counterparts in the `lint` section. \
-        fs::relativize_path(path),
+        Please update the following options in {thing_to_update}:\n  {options_mapping}",
     );
 }
 

crates/ruff_workspace/src/options.rs

@@ -33,7 +33,7 @@ use ruff_python_formatter::{DocstringCodeLineWidth, QuoteStyle};
 
 use crate::settings::LineEnding;
 
-#[derive(Debug, PartialEq, Eq, Default, OptionsMetadata, Serialize, Deserialize)]
+#[derive(Clone, Debug, PartialEq, Eq, Default, OptionsMetadata, Serialize, Deserialize)]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
 pub struct Options {
@@ -441,7 +441,7 @@ pub struct Options {
 ///
 /// Options specified in the `lint` section take precedence over the deprecated top-level settings.
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
-#[derive(Debug, PartialEq, Eq, Default, OptionsMetadata, Serialize, Deserialize)]
+#[derive(Clone, Debug, PartialEq, Eq, Default, OptionsMetadata, Serialize, Deserialize)]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 pub struct LintOptions {
     #[serde(flatten)]
@@ -483,7 +483,7 @@ pub struct LintOptions {
 }
 
 /// Newtype wrapper for [`LintCommonOptions`] that allows customizing the JSON schema and omitting the fields from the [`OptionsMetadata`].
-#[derive(Debug, PartialEq, Eq, Default, Serialize, Deserialize)]
+#[derive(Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize)]
 #[serde(transparent)]
 pub struct DeprecatedTopLevelLintOptions(pub LintCommonOptions);
 
@@ -538,7 +538,7 @@ impl schemars::JsonSchema for DeprecatedTopLevelLintOptions {
 // global settings.
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
 #[derive(
-    Debug, PartialEq, Eq, Default, OptionsMetadata, CombineOptions, Serialize, Deserialize,
+    Clone, Debug, PartialEq, Eq, Default, OptionsMetadata, CombineOptions, Serialize, Deserialize,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 pub struct LintCommonOptions {
@@ -922,7 +922,7 @@ pub struct LintCommonOptions {
 
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
 #[derive(
-    Debug, PartialEq, Eq, Default, OptionsMetadata, CombineOptions, Serialize, Deserialize,
+    Clone, Debug, PartialEq, Eq, Default, OptionsMetadata, CombineOptions, Serialize, Deserialize,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 pub struct Flake8AnnotationsOptions {
@@ -990,7 +990,7 @@ impl Flake8AnnotationsOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1038,7 +1038,7 @@ impl Flake8BanditOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1068,7 +1068,7 @@ impl Flake8BugbearOptions {
     }
 }
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1090,7 +1090,7 @@ impl Flake8BuiltinsOptions {
     }
 }
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1115,7 +1115,7 @@ impl Flake8ComprehensionsOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1169,7 +1169,7 @@ impl Flake8CopyrightOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1188,7 +1188,7 @@ impl Flake8ErrMsgOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1225,7 +1225,7 @@ impl Flake8GetTextOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1258,7 +1258,7 @@ impl Flake8ImplicitStrConcatOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1340,7 +1340,7 @@ impl Flake8ImportConventionsOptions {
     }
 }
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1476,7 +1476,7 @@ impl Flake8PytestStyleOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1548,7 +1548,7 @@ impl Flake8QuotesOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1588,7 +1588,7 @@ impl Flake8SelfOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1645,7 +1645,7 @@ impl Flake8TidyImportsOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1774,7 +1774,7 @@ impl Flake8TypeCheckingOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -1797,7 +1797,7 @@ impl Flake8UnusedArgumentsOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -2400,7 +2400,7 @@ impl IsortOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -2428,7 +2428,7 @@ impl McCabeOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -2520,7 +2520,7 @@ impl Pep8NamingOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -2592,7 +2592,7 @@ impl PycodestyleOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -2682,7 +2682,7 @@ impl PydocstyleOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -2710,7 +2710,7 @@ impl PyflakesOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -2818,7 +2818,7 @@ impl PylintOptions {
 }
 
 #[derive(
-    Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Serialize, Deserialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]
@@ -2874,7 +2874,7 @@ impl PyUpgradeOptions {
 
 /// Configures the way ruff formats your code.
 #[derive(
-    Debug, PartialEq, Eq, Default, Deserialize, Serialize, OptionsMetadata, CombineOptions,
+    Clone, Debug, PartialEq, Eq, Default, Deserialize, Serialize, OptionsMetadata, CombineOptions,
 )]
 #[serde(deny_unknown_fields, rename_all = "kebab-case")]
 #[cfg_attr(feature = "schemars", derive(schemars::JsonSchema))]

crates/ruff_workspace/src/resolver.rs

@@ -264,7 +264,7 @@ fn resolve_configuration(
         let options = pyproject::load_options(&path)?;
 
         let project_root = relativity.resolve(&path);
-        let configuration = Configuration::from_options(options, &path, &project_root)?;
+        let configuration = Configuration::from_options(options, Some(&path), &project_root)?;
 
         // If extending, continue to collect.
         next = configuration.extend.as_ref().map(|extend| {

docs/configuration.md

@@ -449,14 +449,69 @@ Alternatively, pass the notebook file(s) to `ruff` on the command-line directly.
 
 ## Command-line interface
 
-Some configuration options can be provided via the command-line, such as those related to rule
+Some configuration options can be provided or overridden via dedicated flags on the command line.
-enablement and disablement, file discovery, logging level, and more:
+This includes those related to rule enablement and disablement,
+file discovery, logging level, and more:
 
 ```shell
 ruff check path/to/code/ --select F401 --select F403 --quiet
 ```
 
-See `ruff help` for more on Ruff's top-level commands:
+All other configuration options can be set via the command line
+using the `--config` flag, detailed below.
+
+### The `--config` CLI flag
+
+The `--config` flag has two uses. It is most often used to point to the
+configuration file that you would like Ruff to use, for example:
+
+```shell
+ruff check path/to/directory --config path/to/ruff.toml
+```
+
+However, the `--config` flag can also be used to provide arbitrary
+overrides of configuration settings using TOML `<KEY> = <VALUE>` pairs.
+This is mostly useful in situations where you wish to override a configuration setting
+that does not have a dedicated command-line flag.
+
+In the below example, the `--config` flag is the only way of overriding the
+`dummy-variable-rgx` configuration setting from the command line,
+since this setting has no dedicated CLI flag. The `per-file-ignores` setting
+could also have been overridden via the `--per-file-ignores` dedicated flag,
+but using `--config` to override the setting is also fine:
+
+```shell
+ruff check path/to/file --config path/to/ruff.toml --config "lint.dummy-variable-rgx = '__.*'" --config "lint.per-file-ignores = {'some_file.py' = ['F841']}"
+```
+
+Configuration options passed to `--config` are parsed in the same way
+as configuration options in a `ruff.toml` file.
+As such, options specific to the Ruff linter need to be prefixed with `lint.`
+(`--config "lint.dummy-variable-rgx = '__.*'"` rather than simply
+`--config "dummy-variable-rgx = '__.*'"`), and options specific to the Ruff formatter
+need to be prefixed with `format.`.
+
+If a specific configuration option is simultaneously overridden by
+a dedicated flag and by the `--config` flag, the dedicated flag
+takes priority. In this example, the maximum permitted line length
+will be set to 90, not 100:
+
+```shell
+ruff format path/to/file --line-length=90 --config "line-length=100"
+```
+
+Specifying `--config "line-length=90"` will override the `line-length`
+setting from *all* configuration files detected by Ruff,
+including configuration files discovered in subdirectories.
+In this respect, specifying `--config "line-length=90"` has
+the same effect as specifying `--line-length=90`,
+which will similarly override the `line-length` setting from
+all configuration files detected by Ruff, regardless of where
+a specific configuration file is located.
+
+### Full command-line interface
+
+See `ruff help` for the full list of Ruff's top-level commands:
 
 <!-- Begin auto-generated command help. -->
 
@@ -541,9 +596,13 @@ Options:
       --preview
           Enable preview mode; checks will include unstable rules and fixes.
           Use `--no-preview` to disable
-      --config <CONFIG>
+      --config <CONFIG_OPTION>
-          Path to the `pyproject.toml` or `ruff.toml` file to use for
+          Either a path to a TOML configuration file (`pyproject.toml` or
-          configuration
+          `ruff.toml`), or a TOML `<KEY> = <VALUE>` pair (such as you might
+          find in a `ruff.toml` configuration file) overriding a specific
+          configuration option. Overrides of individual settings using this
+          option always take precedence over all configuration files, including
+          configuration files that were also specified using `--config`
       --extension <EXTENSION>
           List of mappings from file extension to language (one of ["python",
           "ipynb", "pyi"]). For example, to treat `.ipy` files as IPython
@@ -640,9 +699,13 @@ Options:
           Avoid writing any formatted files back; instead, exit with a non-zero
           status code and the difference between the current file and how the
           formatted file would look like
-      --config <CONFIG>
+      --config <CONFIG_OPTION>
-          Path to the `pyproject.toml` or `ruff.toml` file to use for
+          Either a path to a TOML configuration file (`pyproject.toml` or
-          configuration
+          `ruff.toml`), or a TOML `<KEY> = <VALUE>` pair (such as you might
+          find in a `ruff.toml` configuration file) overriding a specific
+          configuration option. Overrides of individual settings using this
+          option always take precedence over all configuration files, including
+          configuration files that were also specified using `--config`
       --extension <EXTENSION>
           List of mappings from file extension to language (one of ["python",
           "ipynb", "pyi"]). For example, to treat `.ipy` files as IPython