remove information we don't need anymore and DRY the business logic

crates/biome_cli/src/execute/process_file/assists.rs

@@ -3,6 +3,7 @@ use crate::execute::process_file::workspace_file::WorkspaceFile;
 use crate::execute::process_file::{
     DiffKind, FileResult, FileStatus, Message, SharedTraversalOptions,
 };
+use biome_analyze::RuleCategoriesBuilder;
 use biome_diagnostics::category;
 use biome_service::file_handlers::{AstroFileHandler, SvelteFileHandler, VueFileHandler};
 use biome_service::workspace::FixFileMode;
@@ -19,10 +20,16 @@ pub(crate) fn assists_with_guard<'ctx>(
             let skip = Vec::new();
             let fix_result = workspace_file
                 .guard()
-                .fix_file(FixFileMode::SafeFixes, false, only.clone(), skip.clone())
+                .fix_file(
+                    FixFileMode::SafeFixes,
+                    false,
+                    RuleCategoriesBuilder::default().with_action().build(),
+                    only.clone(),
+                    skip.clone(),
+                )
                 .with_file_path_and_code(
                     workspace_file.path.display().to_string(),
-                    category!("lint"),
+                    category!("assists"),
                 )?;
 
             ctx.push_message(Message::SkippedFixes {

crates/biome_cli/src/execute/process_file/lint.rs

@@ -31,7 +31,16 @@ pub(crate) fn lint_with_guard<'ctx>(
             if let Some(fix_mode) = ctx.execution.as_fix_file_mode() {
                 let fix_result = workspace_file
                     .guard()
-                    .fix_file(*fix_mode, false, only.clone(), skip.clone())
+                    .fix_file(
+                        *fix_mode,
+                        false,
+                        RuleCategoriesBuilder::default()
+                            .with_syntax()
+                            .with_lint()
+                            .build(),
+                        only.clone(),
+                        skip.clone(),
+                    )
                     .with_file_path_and_code(
                         workspace_file.path.display().to_string(),
                         category!("lint"),

crates/biome_cli/src/execute/std_in.rs

@@ -122,6 +122,10 @@ pub(crate) fn run<'a>(
                     should_format: mode.is_check() && file_features.supports_format(),
                     only: only.clone(),
                     skip: skip.clone(),
+                    rule_categories: RuleCategoriesBuilder::default()
+                        .with_syntax()
+                        .with_lint()
+                        .build(),
                 })?;
                 let code = fix_file_result.code;
                 let output = match biome_path.extension_as_str() {

crates/biome_cli/tests/snapshots/main_cases_assists/json_sort_keys.snap

@@ -0,0 +1,44 @@
+---
+source: crates/biome_cli/tests/snap_test.rs
+expression: content
+---
+## `biome.json`
+
+```json
+{ "assists": { "enabled": true }, "formatter": { "enabled": false } }
+```
+
+## `file.json`
+
+```json
+{ "zod": true, "lorem": "ipsum", "foo": "bar" }
+```
+
+# Termination Message
+
+```block
+check ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+  × Some errors were emitted while running checks.
+  
+
+
+```
+
+# Emitted Messages
+
+```block
+file.json assists ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+  × Not all assists were applied:
+  
+  - {·"zod":·true,·"lorem":·"ipsum",·"foo":·"bar"·}
+  + {·"foo":·"bar"·,"lorem":·"ipsum","zod":·true·}
+  
+
+```
+
+```block
+Checked 1 file in <TIME>. No fixes applied.
+Found 1 error.
+```

crates/biome_cli/tests/snapshots/main_commands_check/file_too_large.snap

@@ -33,6 +33,16 @@ check.js organizeImports ━━━━━━━━━━━━━━━━━━
     Use the `files.maxSize` configuration to change the maximum size of files processed.
   
 
+```
+
+```block
+check.js assists ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+  × Size of check.js is 1.0 MiB which exceeds configured maximum of 1.0 MiB for this project.
+    The file size limit exists to prevent us inadvertently slowing down and loading large files that we shouldn't.
+    Use the `files.maxSize` configuration to change the maximum size of files processed.
+  
+
 ```
 
 ```block

crates/biome_cli/tests/snapshots/main_commands_check/file_too_large_cli_limit.snap

@@ -40,6 +40,16 @@ check.js organizeImports ━━━━━━━━━━━━━━━━━━
     Use the `files.maxSize` configuration to change the maximum size of files processed.
   
 
+```
+
+```block
+check.js assists ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+  × Size of check.js is 27 B which exceeds configured maximum of 16 B for this project.
+    The file size limit exists to prevent us inadvertently slowing down and loading large files that we shouldn't.
+    Use the `files.maxSize` configuration to change the maximum size of files processed.
+  
+
 ```
 
 ```block

crates/biome_cli/tests/snapshots/main_commands_check/file_too_large_config_limit.snap

@@ -50,6 +50,16 @@ check.js organizeImports ━━━━━━━━━━━━━━━━━━
     Use the `files.maxSize` configuration to change the maximum size of files processed.
   
 
+```
+
+```block
+check.js assists ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+  × Size of check.js is 27 B which exceeds configured maximum of 16 B for this project.
+    The file size limit exists to prevent us inadvertently slowing down and loading large files that we shouldn't.
+    Use the `files.maxSize` configuration to change the maximum size of files processed.
+  
+
 ```
 
 ```block

crates/biome_cli/tests/snapshots/main_commands_ci/file_too_large.snap

@@ -33,6 +33,16 @@ ci.js organizeImports ━━━━━━━━━━━━━━━━━━━
     Use the `files.maxSize` configuration to change the maximum size of files processed.
   
 
+```
+
+```block
+ci.js assists ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+  × Size of ci.js is 1.0 MiB which exceeds configured maximum of 1.0 MiB for this project.
+    The file size limit exists to prevent us inadvertently slowing down and loading large files that we shouldn't.
+    Use the `files.maxSize` configuration to change the maximum size of files processed.
+  
+
 ```
 
 ```block

crates/biome_cli/tests/snapshots/main_commands_ci/file_too_large_cli_limit.snap

@@ -40,6 +40,16 @@ ci.js organizeImports ━━━━━━━━━━━━━━━━━━━
     Use the `files.maxSize` configuration to change the maximum size of files processed.
   
 
+```
+
+```block
+ci.js assists ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+  × Size of ci.js is 27 B which exceeds configured maximum of 16 B for this project.
+    The file size limit exists to prevent us inadvertently slowing down and loading large files that we shouldn't.
+    Use the `files.maxSize` configuration to change the maximum size of files processed.
+  
+
 ```
 
 ```block

crates/biome_cli/tests/snapshots/main_commands_ci/file_too_large_config_limit.snap

@@ -50,6 +50,16 @@ ci.js organizeImports ━━━━━━━━━━━━━━━━━━━
     Use the `files.maxSize` configuration to change the maximum size of files processed.
   
 
+```
+
+```block
+ci.js assists ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+  × Size of ci.js is 27 B which exceeds configured maximum of 16 B for this project.
+    The file size limit exists to prevent us inadvertently slowing down and loading large files that we shouldn't.
+    Use the `files.maxSize` configuration to change the maximum size of files processed.
+  
+
 ```
 
 ```block

crates/biome_lsp/src/handlers/analysis.rs

@@ -3,7 +3,7 @@ use crate::converters::line_index::LineIndex;
 use crate::session::Session;
 use crate::utils;
 use anyhow::{Context, Result};
-use biome_analyze::{ActionCategory, SourceActionKind};
+use biome_analyze::{ActionCategory, RuleCategoriesBuilder, SourceActionKind};
 use biome_diagnostics::Applicability;
 use biome_fs::BiomePath;
 use biome_rowan::{TextRange, TextSize};
@@ -243,6 +243,10 @@ fn fix_all(
         should_format,
         only: vec![],
         skip: vec![],
+        rule_categories: RuleCategoriesBuilder::default()
+            .with_syntax()
+            .with_lint()
+            .build(),
     })?;
 
     if fixed.actions.is_empty() {

crates/biome_service/src/file_handlers/css.rs

@@ -35,7 +35,7 @@ use biome_parser::AnyParse;
 use biome_rowan::{AstNode, NodeCache};
 use biome_rowan::{TextRange, TextSize, TokenAtOffset};
 use std::borrow::Cow;
-use tracing::{debug_span, error, info, trace, trace_span};
+use tracing::{debug_span, error, info, trace_span};
 
 #[derive(Debug, Clone, serde::Serialize, serde::Deserialize)]
 #[cfg_attr(feature = "schema", derive(schemars::JsonSchema))]
@@ -463,41 +463,41 @@ pub(crate) fn code_actions(params: CodeActionsParams) -> PullActionsResult {
         path,
         manifest: _,
         language,
-        settings,
-        only: _,
-        skip: _,
+        only,
+        skip,
     } = params;
     debug_span!("Code actions CSS", range =? range, path =? path).in_scope(move || {
         let tree = parse.tree();
         trace_span!("Parsed file", tree =? tree).in_scope(move || {
-            let rules = settings.as_linter_rules(params.path.as_path());
-            let filter = rules
-                .as_ref()
-                .map(|rules| rules.as_enabled_rules())
-                .unwrap_or_default()
-                .into_iter()
-                .collect::<Vec<_>>();
-
-            let mut filter = AnalysisFilter::from_enabled_rules(filter.as_slice());
-
-            let mut categories = RuleCategoriesBuilder::default().with_syntax().with_lint();
-            if settings.organize_imports.enabled {
-                categories = categories.with_action();
-            }
-            filter.categories = categories.build();
-            filter.range = range;
-
-            let analyzer_options = workspace.analyzer_options::<CssLanguage>(path, &language);
-
             let Some(_) = language.to_css_file_source() else {
                 error!("Could not determine the file source of the file");
                 return PullActionsResult {
                     actions: Vec::new(),
                 };
             };
 
-            trace!("CSS runs the analyzer");
+            let analyzer_options = workspace.analyzer_options::<CssLanguage>(path, &language);
             let mut actions = Vec::new();
+            let mut lint_visitor =
+                LintVisitor::new(&only, &skip, workspace.settings(), path.as_path());
+            let mut syntax_visitor = SyntaxVisitor::default();
+            biome_js_analyze::visit_registry(&mut lint_visitor);
+            biome_js_analyze::visit_registry(&mut syntax_visitor);
+            let (mut enabled_rules, disabled_rules) = lint_visitor.finish();
+            enabled_rules.extend(syntax_visitor.enabled_rules);
+
+            let filter = AnalysisFilter {
+                categories: RuleCategoriesBuilder::default()
+                    .with_syntax()
+                    .with_lint()
+                    .with_action()
+                    .build(),
+                enabled_rules: Some(enabled_rules.as_slice()),
+                disabled_rules: &disabled_rules,
+                range,
+            };
+
+            info!("CSS runs the analyzer");
 
             analyze(&tree, filter, &analyzer_options, |signal| {
                 actions.extend(signal.actions().into_code_action_iter().map(|item| {

crates/biome_service/src/file_handlers/graphql.rs

@@ -33,7 +33,7 @@ use biome_graphql_syntax::{GraphqlLanguage, GraphqlRoot, GraphqlSyntaxNode, Text
 use biome_parser::AnyParse;
 use biome_rowan::{AstNode, NodeCache, TokenAtOffset};
 use std::borrow::Cow;
-use tracing::{debug_span, error, info, trace, trace_span};
+use tracing::{debug_span, error, info, trace_span};
 
 #[derive(Debug, Clone, serde::Serialize, serde::Deserialize)]
 #[cfg_attr(feature = "schema", derive(schemars::JsonSchema))]
@@ -416,41 +416,41 @@ pub(crate) fn code_actions(params: CodeActionsParams) -> PullActionsResult {
         path,
         manifest: _,
         language,
-        settings,
         only,
         skip,
     } = params;
     debug_span!("Code actions GraphQL", range =? range, path =? path).in_scope(move || {
         let tree = parse.tree();
         trace_span!("Parsed file", tree =? tree).in_scope(move || {
-            let rules = settings.as_linter_rules(params.path.as_path());
-            let filter = rules
-                .as_ref()
-                .map(|rules| rules.as_enabled_rules())
-                .unwrap_or_default()
-                .into_iter()
-                .collect::<Vec<_>>();
-
-            let mut filter = AnalysisFilter::from_enabled_rules(filter.as_slice());
-
-            let mut categories = RuleCategoriesBuilder::default().with_syntax().with_lint();
-            if settings.organize_imports.enabled {
-                categories = categories.with_action();
-            }
-            filter.categories = categories.build();
-            filter.range = range;
-
-            let analyzer_options = workspace.analyzer_options::<GraphqlLanguage>(path, &language);
-
             let Some(_) = language.to_graphql_file_source() else {
                 error!("Could not determine the file source of the file");
                 return PullActionsResult {
                     actions: Vec::new(),
                 };
             };
 
-            trace!("GraphQL runs the analyzer");
+            let analyzer_options = workspace.analyzer_options::<GraphqlLanguage>(path, &language);
             let mut actions = Vec::new();
+            let mut lint_visitor =
+                LintVisitor::new(&only, &skip, workspace.settings(), path.as_path());
+            let mut syntax_visitor = SyntaxVisitor::default();
+            biome_js_analyze::visit_registry(&mut lint_visitor);
+            biome_js_analyze::visit_registry(&mut syntax_visitor);
+            let (mut enabled_rules, disabled_rules) = lint_visitor.finish();
+            enabled_rules.extend(syntax_visitor.enabled_rules);
+
+            let filter = AnalysisFilter {
+                categories: RuleCategoriesBuilder::default()
+                    .with_syntax()
+                    .with_lint()
+                    .with_action()
+                    .build(),
+                enabled_rules: Some(enabled_rules.as_slice()),
+                disabled_rules: &disabled_rules,
+                range,
+            };
+
+            info!("GraphQL runs the analyzer");
 
             analyze(&tree, filter, &analyzer_options, |signal| {
                 actions.extend(signal.actions().into_code_action_iter().map(|item| {

crates/biome_service/src/file_handlers/javascript.rs

@@ -21,8 +21,8 @@ use crate::{
 };
 use biome_analyze::options::PreferredQuote;
 use biome_analyze::{
-    AnalysisFilter, AnalyzerConfiguration, AnalyzerOptions, ControlFlow, Never,
-    RuleCategoriesBuilder, RuleCategory, RuleError,
+    AnalysisFilter, AnalyzerConfiguration, AnalyzerOptions, ControlFlow, Never, QueryMatch,
+    RuleCategoriesBuilder, RuleCategory, RuleError, RuleFilter,
 };
 use biome_configuration::javascript::JsxRuntime;
 use biome_diagnostics::{category, Applicability, Diagnostic, DiagnosticExt, Severity};
@@ -539,7 +539,6 @@ pub(crate) fn code_actions(params: CodeActionsParams) -> PullActionsResult {
         path,
         manifest,
         language,
-        settings,
         only,
         skip,
     } = params;
@@ -629,10 +628,7 @@ pub(crate) fn fix_all(params: FixAllParams) -> Result<FixFileResult, WorkspaceEr
     enabled_rules.extend(syntax_visitor.enabled_rules);
 
     let filter = AnalysisFilter {
-        categories: RuleCategoriesBuilder::default()
-            .with_syntax()
-            .with_lint()
-            .build(),
+        categories: params.rule_categories,
         enabled_rules: Some(enabled_rules.as_slice()),
         disabled_rules: &disabled_rules,
         range: None,