Fix RUF100 to detect unused file-level noqa directives with specific codes (#17042) (#17061)

Closes #17042

## Summary
This PR fixes the issue outlined in #17042 where RUF100 (unused-noqa)
fails to detect unused file-level noqa directives (`# ruff: noqa` or `#
ruff: noqa: {code}`).

The issue stems from two underlying causes:

1. For blanket file-level directives (`# ruff: noqa`), there's a
circular dependency: the directive exempts all rules including RUF100
itself, which prevents checking for usage. This isn't changed by this
PR. I would argue it is intendend behavior - a blanket `# ruff: noqa`
directive should exempt all rules including RUF100 itself.

2. For code-specific file-level directives (e.g. `# ruff: noqa: F841`),
the handling was missing in the `check_noqa` function. This is added in
this PR.

## Notes
- For file-level directives, the `matches` array is pre-populated with
the specified codes during parsing, unlike line-level directives which
only populate their `matches` array when actually suppressing
diagnostics. This difference requires the somewhat clunky handling of
both cases. I would appreciate guidance on a cleaner design :)

- A more fundamental solution would be to change how file-level
directives initialize the `matches` array in
`FileNoqaDirectives::extract()`, but that requires more substantial
changes as it breaks existing functionality. I suspect discussions in
#16483 are relevant for this.

## Test Plan
- Local verification
- Added a test case and fixture

crates/ruff_linter/resources/test/fixtures/ruff/RUF100_6.py

@@ -0,0 +1 @@
+# ruff: noqa: F841 -- intentional unused file directive; will be removed

crates/ruff_linter/resources/test/fixtures/ruff/RUF100_7.py

@@ -0,0 +1,8 @@
+# flake8: noqa: F841, E501 -- used followed by unused code
+# ruff: noqa: E701, F541 -- unused followed by used code
+
+
+def a():
+    # Violating noqa'd F841 (unused) and F541 (no-placeholder f-string)
+    x = f"Hello, world"
+    return 6

crates/ruff_linter/src/checkers/noqa.rs

@@ -110,10 +110,29 @@ pub(crate) fn check_noqa(
         && !exemption.includes(Rule::UnusedNOQA)
         && !per_file_ignores.contains(Rule::UnusedNOQA)
     {
-        for line in noqa_directives.lines() {
-            match &line.directive {
+        let directives: Vec<_> = if settings.preview.is_enabled() {
+            noqa_directives
+                .lines()
+                .iter()
+                .map(|line| (&line.directive, &line.matches, false))
+                .chain(
+                    file_noqa_directives
+                        .lines()
+                        .iter()
+                        .map(|line| (&line.parsed_file_exemption, &line.matches, true)),
+                )
+                .collect()
+        } else {
+            noqa_directives
+                .lines()
+                .iter()
+                .map(|line| (&line.directive, &line.matches, false))
+                .collect()
+        };
+        for (directive, matches, is_file_level) in directives {
+            match directive {
                 Directive::All(directive) => {
-                    if line.matches.is_empty() {
+                    if matches.is_empty() {
                         let edit = delete_comment(directive.range(), locator);
                         let mut diagnostic =
                             Diagnostic::new(UnusedNOQA { codes: None }, directive.range());
@@ -137,17 +156,21 @@ pub(crate) fn check_noqa(
                             break;
                         }
 
-                        if !seen_codes.insert(original_code) {
-                            duplicated_codes.push(original_code);
-                        } else if line.matches.iter().any(|match_| *match_ == code)
-                            || settings
+                        if seen_codes.insert(original_code) {
+                            let is_code_used = if is_file_level {
+                                diagnostics
+                                    .iter()
+                                    .any(|diag| diag.kind.rule().noqa_code() == code)
+                            } else {
+                                matches.iter().any(|match_| *match_ == code)
+                            } || settings
                                 .external
                                 .iter()
-                                .any(|external| code.starts_with(external))
-                        {
-                            valid_codes.push(original_code);
-                        } else {
-                            if let Ok(rule) = Rule::from_code(code) {
+                                .any(|external| code.starts_with(external));
+
+                            if is_code_used {
+                                valid_codes.push(original_code);
+                            } else if let Ok(rule) = Rule::from_code(code) {
                                 if settings.rules.enabled(rule) {
                                     unmatched_codes.push(original_code);
                                 } else {
@@ -156,6 +179,8 @@ pub(crate) fn check_noqa(
                             } else {
                                 unknown_codes.push(original_code);
                             }
+                        } else {
+                            duplicated_codes.push(original_code);
                         }
                     }
 
@@ -171,8 +196,18 @@ pub(crate) fn check_noqa(
                         let edit = if valid_codes.is_empty() {
                             delete_comment(directive.range(), locator)
                         } else {
+                            let original_text = locator.slice(directive.range());
+                            let prefix = if is_file_level {
+                                if original_text.contains("flake8") {
+                                    "# flake8: noqa: "
+                                } else {
+                                    "# ruff: noqa: "
+                                }
+                            } else {
+                                "# noqa: "
+                            };
                             Edit::range_replacement(
-                                format!("# noqa: {}", valid_codes.join(", ")),
+                                format!("{}{}", prefix, valid_codes.join(", ")),
                                 directive.range(),
                             )
                         };

crates/ruff_linter/src/rules/ruff/mod.rs

@@ -315,6 +315,37 @@ mod tests {
         Ok(())
     }
 
+    #[test]
+    fn ruff_noqa_filedirective_unused() -> Result<()> {
+        let diagnostics = test_path(
+            Path::new("ruff/RUF100_6.py"),
+            &settings::LinterSettings {
+                preview: PreviewMode::Enabled,
+                ..settings::LinterSettings::for_rules(vec![Rule::UnusedNOQA])
+            },
+        )?;
+        assert_messages!(diagnostics);
+        Ok(())
+    }
+
+    #[test]
+    fn ruff_noqa_filedirective_unused_last_of_many() -> Result<()> {
+        let diagnostics = test_path(
+            Path::new("ruff/RUF100_7.py"),
+            &settings::LinterSettings {
+                preview: PreviewMode::Enabled,
+                ..settings::LinterSettings::for_rules(vec![
+                    Rule::UnusedNOQA,
+                    Rule::FStringMissingPlaceholders,
+                    Rule::LineTooLong,
+                    Rule::UnusedVariable,
+                ])
+            },
+        )?;
+        assert_messages!(diagnostics);
+        Ok(())
+    }
+
     #[test]
     fn invalid_rule_code_external_rules() -> Result<()> {
         let diagnostics = test_path(
@@ -324,7 +355,6 @@ mod tests {
                 ..settings::LinterSettings::for_rule(Rule::InvalidRuleCode)
             },
         )?;
-
         assert_messages!(diagnostics);
         Ok(())
     }

crates/ruff_linter/src/rules/ruff/snapshots/ruff_linter__rules__ruff__tests__ruff_noqa_filedirective_unused.snap

@@ -0,0 +1,13 @@
+---
+source: crates/ruff_linter/src/rules/ruff/mod.rs
+---
+RUF100_6.py:1:1: RUF100 [*] Unused `noqa` directive (non-enabled: `F841`)
+  |
+1 | # ruff: noqa: F841 -- intentional unused file directive; will be removed
+  | ^^^^^^^^^^^^^^^^^^ RUF100
+  |
+  = help: Remove unused `noqa` directive
+
+ℹ Safe fix
+1   |-# ruff: noqa: F841 -- intentional unused file directive; will be removed
+  1 |+

crates/ruff_linter/src/rules/ruff/snapshots/ruff_linter__rules__ruff__tests__ruff_noqa_filedirective_unused_last_of_many.snap

@@ -0,0 +1,33 @@
+---
+source: crates/ruff_linter/src/rules/ruff/mod.rs
+---
+RUF100_7.py:1:1: RUF100 [*] Unused `noqa` directive (unused: `E501`)
+  |
+1 | # flake8: noqa: F841, E501 -- used followed by unused code
+  | ^^^^^^^^^^^^^^^^^^^^^^^^^^ RUF100
+2 | # ruff: noqa: E701, F541 -- unused followed by used code
+  |
+  = help: Remove unused `noqa` directive
+
+ℹ Safe fix
+1   |-# flake8: noqa: F841, E501 -- used followed by unused code
+  1 |+# flake8: noqa: F841 -- used followed by unused code
+2 2 | # ruff: noqa: E701, F541 -- unused followed by used code
+3 3 | 
+4 4 | 
+
+RUF100_7.py:2:1: RUF100 [*] Unused `noqa` directive (non-enabled: `E701`)
+  |
+1 | # flake8: noqa: F841, E501 -- used followed by unused code
+2 | # ruff: noqa: E701, F541 -- unused followed by used code
+  | ^^^^^^^^^^^^^^^^^^^^^^^^ RUF100
+  |
+  = help: Remove unused `noqa` directive
+
+ℹ Safe fix
+1 1 | # flake8: noqa: F841, E501 -- used followed by unused code
+2   |-# ruff: noqa: E701, F541 -- unused followed by used code
+  2 |+# ruff: noqa: F541 -- unused followed by used code
+3 3 | 
+4 4 | 
+5 5 | def a():