Support disabling tool suggest for specific tools. (#20072)

## Summary
- Add `disable_tool_suggest` to app and plugin config, schema, and
TypeScript output
- Exclude disabled connectors and plugins from tool suggestion discovery
- Persist "never show again" tool-suggestion choices back into
`config.toml`
- Update config docs and add coverage for connector and plugin
suppression

## Testing
- Added and updated unit tests for config persistence and tool-suggest
filtering
- Not run (not requested)

codex-rs/core/src/config/mod.rs

@@ -46,6 +46,7 @@ use codex_config::types::OtelConfig;
 use codex_config::types::OtelConfigToml;
 use codex_config::types::OtelExporterKind;
 use codex_config::types::ToolSuggestConfig;
+use codex_config::types::ToolSuggestDisabledTool;
 use codex_config::types::ToolSuggestDiscoverable;
 use codex_config::types::TuiKeymap;
 use codex_config::types::TuiNotificationSettings;
@@ -95,6 +96,7 @@ use codex_utils_absolute_path::AbsolutePathBufGuard;
 use serde::Deserialize;
 use std::collections::BTreeMap;
 use std::collections::HashMap;
+use std::collections::HashSet;
 use std::io::ErrorKind;
 use std::path::Path;
 use std::path::PathBuf;
@@ -1416,10 +1418,29 @@ pub struct AgentRoleConfig {
     pub nickname_candidates: Option<Vec<String>>,
 }
 
-fn resolve_tool_suggest_config(config_toml: &ConfigToml) -> ToolSuggestConfig {
-    let discoverables = config_toml
-        .tool_suggest
-        .as_ref()
+fn resolve_tool_suggest_config(
+    config_toml: &ConfigToml,
+    config_layer_stack: &ConfigLayerStack,
+) -> ToolSuggestConfig {
+    resolve_tool_suggest_config_from_config(config_toml.tool_suggest.as_ref(), config_layer_stack)
+}
+
+pub(crate) fn resolve_tool_suggest_config_from_layer_stack(
+    config_layer_stack: &ConfigLayerStack,
+) -> ToolSuggestConfig {
+    let tool_suggest = config_layer_stack
+        .effective_config()
+        .get("tool_suggest")
+        .cloned()
+        .and_then(|value| value.try_into::<ToolSuggestConfig>().ok());
+    resolve_tool_suggest_config_from_config(tool_suggest.as_ref(), config_layer_stack)
+}
+
+fn resolve_tool_suggest_config_from_config(
+    tool_suggest: Option<&ToolSuggestConfig>,
+    config_layer_stack: &ConfigLayerStack,
+) -> ToolSuggestConfig {
+    let discoverables = tool_suggest
         .into_iter()
         .flat_map(|tool_suggest| tool_suggest.discoverables.iter())
         .filter_map(|discoverable| {
@@ -1434,8 +1455,47 @@ fn resolve_tool_suggest_config(config_toml: &ConfigToml) -> ToolSuggestConfig {
             }
         })
         .collect();
+    let mut seen_disabled_tools = HashSet::new();
+    let mut disabled_tools = Vec::new();
+    let mut add_disabled_tool = |disabled_tool: ToolSuggestDisabledTool| {
+        if let Some(disabled_tool) = disabled_tool.normalized()
+            && seen_disabled_tools.insert(disabled_tool.clone())
+        {
+            disabled_tools.push(disabled_tool);
+        }
+    };
 
-    ToolSuggestConfig { discoverables }
+    let layers = config_layer_stack.get_layers(
+        ConfigLayerStackOrdering::LowestPrecedenceFirst,
+        /*include_disabled*/ false,
+    );
+    if layers.is_empty() {
+        for disabled_tool in tool_suggest
+            .into_iter()
+            .flat_map(|tool_suggest| tool_suggest.disabled_tools.iter().cloned())
+        {
+            add_disabled_tool(disabled_tool);
+        }
+    } else {
+        for layer in layers {
+            let Some(tool_suggest) = layer
+                .config
+                .get("tool_suggest")
+                .cloned()
+                .and_then(|value| value.try_into::<ToolSuggestConfig>().ok())
+            else {
+                continue;
+            };
+            for disabled_tool in tool_suggest.disabled_tools {
+                add_disabled_tool(disabled_tool);
+            }
+        }
+    }
+
+    ToolSuggestConfig {
+        discoverables,
+        disabled_tools,
+    }
 }
 
 fn thread_store_config(
@@ -1840,7 +1900,7 @@ impl Config {
                 .clone(),
             None => ConfigProfile::default(),
         };
-        let tool_suggest = resolve_tool_suggest_config(&cfg);
+        let tool_suggest = resolve_tool_suggest_config(&cfg, &config_layer_stack);
         let feature_overrides = FeatureOverrides {
             include_apply_patch_tool: include_apply_patch_tool_override,
             web_search_request: override_tools_web_search_request,