diff --git a/crates/ruff_cli/src/commands/mod.rs b/crates/ruff_cli/src/commands/mod.rs
index bc08aa1cd8..cbe30fd5c5 100644
--- a/crates/ruff_cli/src/commands/mod.rs
+++ b/crates/ruff_cli/src/commands/mod.rs
@@ -1,18 +1,9 @@
-pub use add_noqa::add_noqa;
-pub use clean::clean;
-pub use linter::linter;
-pub use rule::rule;
-pub use run::run;
-pub use run_stdin::run_stdin;
-pub use show_files::show_files;
-pub use show_settings::show_settings;
-
-mod add_noqa;
-mod clean;
+pub mod add_noqa;
+pub mod clean;
 pub mod config;
-mod linter;
-mod rule;
-mod run;
-mod run_stdin;
-mod show_files;
-mod show_settings;
+pub mod linter;
+pub mod rule;
+pub mod run;
+pub mod run_stdin;
+pub mod show_files;
+pub mod show_settings;
diff --git a/crates/ruff_cli/src/main.rs b/crates/ruff_cli/src/main.rs
index d8ed2bc85e..899f59734b 100644
--- a/crates/ruff_cli/src/main.rs
+++ b/crates/ruff_cli/src/main.rs
@@ -100,10 +100,10 @@ quoting the executed command, along with the relevant file contents and `pyproje
     set_up_logging(&log_level)?;
 
     match command {
-        Command::Rule { rule, format } => commands::rule(&rule, format)?,
+        Command::Rule { rule, format } => commands::rule::rule(&rule, format)?,
         Command::Config { option } => return Ok(commands::config::config(option.as_deref())),
-        Command::Linter { format } => commands::linter(format)?,
-        Command::Clean => commands::clean(log_level)?,
+        Command::Linter { format } => commands::linter::linter(format)?,
+        Command::Clean => commands::clean::clean(log_level)?,
         Command::GenerateShellCompletion { shell } => {
             shell.generate(&mut Args::command(), &mut io::stdout());
         }
@@ -126,11 +126,11 @@ fn check(args: CheckArgs, log_level: LogLevel) -> Result<ExitStatus> {
     )?;
 
     if cli.show_settings {
-        commands::show_settings(&cli.files, &pyproject_strategy, &overrides)?;
+        commands::show_settings::show_settings(&cli.files, &pyproject_strategy, &overrides)?;
         return Ok(ExitStatus::Success);
     }
     if cli.show_files {
-        commands::show_files(&cli.files, &pyproject_strategy, &overrides)?;
+        commands::show_files::show_files(&cli.files, &pyproject_strategy, &overrides)?;
         return Ok(ExitStatus::Success);
     }
 
@@ -184,7 +184,8 @@ fn check(args: CheckArgs, log_level: LogLevel) -> Result<ExitStatus> {
         if !matches!(autofix, fix::FixMode::None) {
             warn_user_once!("--fix is incompatible with --add-noqa.");
         }
-        let modifications = commands::add_noqa(&cli.files, &pyproject_strategy, &overrides)?;
+        let modifications =
+            commands::add_noqa::add_noqa(&cli.files, &pyproject_strategy, &overrides)?;
         if modifications > 0 && log_level >= LogLevel::Default {
             #[allow(clippy::print_stderr)]
             {
@@ -208,7 +209,7 @@ fn check(args: CheckArgs, log_level: LogLevel) -> Result<ExitStatus> {
         Printer::clear_screen()?;
         printer.write_to_user("Starting linter in watch mode...\n");
 
-        let messages = commands::run(
+        let messages = commands::run::run(
             &cli.files,
             &pyproject_strategy,
             &overrides,
@@ -237,7 +238,7 @@ fn check(args: CheckArgs, log_level: LogLevel) -> Result<ExitStatus> {
                         Printer::clear_screen()?;
                         printer.write_to_user("File change detected...\n");
 
-                        let messages = commands::run(
+                        let messages = commands::run::run(
                             &cli.files,
                             &pyproject_strategy,
                             &overrides,
@@ -255,14 +256,14 @@ fn check(args: CheckArgs, log_level: LogLevel) -> Result<ExitStatus> {
 
         // Generate lint violations.
         let diagnostics = if is_stdin {
-            commands::run_stdin(
+            commands::run_stdin::run_stdin(
                 cli.stdin_filename.map(fs::normalize_path).as_deref(),
                 &pyproject_strategy,
                 &overrides,
                 autofix,
             )?
         } else {
-            commands::run(
+            commands::run::run(
                 &cli.files,
                 &pyproject_strategy,
                 &overrides,