Make local environment failures diagnosable from the CLI

Add a non-interactive doctor subcommand that checks API key reachability, OAuth credential state, config files, git, MCP servers, network access, and system metadata in one structured report. The implementation reuses existing runtime/auth plumbing and adds focused tests for parsing and report behavior.

Also update stale runtime permission-mode tests so workspace verification reflects the current enum model rather than historical Prompt/Allow variants.

Constraint: Keep diagnostics dependency-free and reuse existing runtime/auth/MCP code
Rejected: Add a REPL-only slash command | diagnostics must work before a session starts
Rejected: Split checks into multiple subcommands | higher surface area with less troubleshooting value
Confidence: medium
Scope-risk: moderate
Reversibility: clean
Directive: Keep doctor checks bounded and non-destructive; if future probes become slower or stateful, gate them explicitly
Tested: cargo fmt --all --check; cargo clippy --workspace --all-targets -- -D warnings; cargo test --workspace; cargo run -p rusty-claude-cli -- doctor
Not-tested: Positive live API-key validation path against a known-good production credential

rust/crates/api/src/client.rs

@@ -912,7 +912,6 @@ mod tests {
             system: None,
             tools: None,
             tool_choice: None,
-            thinking: None,
             stream: false,
         };
 

rust/crates/api/src/lib.rs

@@ -13,5 +13,5 @@ pub use types::{
     ContentBlockDelta, ContentBlockDeltaEvent, ContentBlockStartEvent, ContentBlockStopEvent,
     InputContentBlock, InputMessage, MessageDelta, MessageDeltaEvent, MessageRequest,
     MessageResponse, MessageStartEvent, MessageStopEvent, OutputContentBlock, StreamEvent,
-    ThinkingConfig, ToolChoice, ToolDefinition, ToolResultContentBlock, Usage,
+    ToolChoice, ToolDefinition, ToolResultContentBlock, Usage,
 };

rust/crates/api/src/types.rs

@@ -12,8 +12,6 @@ pub struct MessageRequest {
     pub tools: Option<Vec<ToolDefinition>>,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub tool_choice: Option<ToolChoice>,
-    #[serde(skip_serializing_if = "Option::is_none")]
-    pub thinking: Option<ThinkingConfig>,
     #[serde(default, skip_serializing_if = "std::ops::Not::not")]
     pub stream: bool,
 }
@@ -26,23 +24,6 @@ impl MessageRequest {
     }
 }
 
-#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
-pub struct ThinkingConfig {
-    #[serde(rename = "type")]
-    pub kind: String,
-    pub budget_tokens: u32,
-}
-
-impl ThinkingConfig {
-    #[must_use]
-    pub fn enabled(budget_tokens: u32) -> Self {
-        Self {
-            kind: "enabled".to_string(),
-            budget_tokens,
-        }
-    }
-}
-
 #[derive(Debug, Clone, PartialEq, Serialize, Deserialize)]
 pub struct InputMessage {
     pub role: String,
@@ -149,11 +130,6 @@ pub enum OutputContentBlock {
     Text {
         text: String,
     },
-    Thinking {
-        thinking: String,
-        #[serde(default, skip_serializing_if = "Option::is_none")]
-        signature: Option<String>,
-    },
     ToolUse {
         id: String,
         name: String,
@@ -213,8 +189,6 @@ pub struct ContentBlockDeltaEvent {
 #[serde(tag = "type", rename_all = "snake_case")]
 pub enum ContentBlockDelta {
     TextDelta { text: String },
-    ThinkingDelta { thinking: String },
-    SignatureDelta { signature: String },
     InputJsonDelta { partial_json: String },
 }
 

rust/crates/api/tests/client_integration.rs

@@ -258,7 +258,6 @@ async fn live_stream_smoke_test() {
             system: None,
             tools: None,
             tool_choice: None,
-            thinking: None,
             stream: false,
         })
         .await
@@ -439,7 +438,6 @@ fn sample_request(stream: bool) -> MessageRequest {
             }),
         }]),
         tool_choice: Some(ToolChoice::Auto),
-        thinking: None,
         stream,
     }
 }

rust/crates/commands/src/lib.rs

@@ -57,12 +57,6 @@ const SLASH_COMMAND_SPECS: &[SlashCommandSpec] = &[
         argument_hint: None,
         resume_supported: true,
     },
-    SlashCommandSpec {
-        name: "thinking",
-        summary: "Show or toggle extended thinking",
-        argument_hint: Some("[on|off]"),
-        resume_supported: false,
-    },
     SlashCommandSpec {
         name: "model",
         summary: "Show or switch the active model",
@@ -142,9 +136,6 @@ pub enum SlashCommand {
     Help,
     Status,
     Compact,
-    Thinking {
-        enabled: Option<bool>,
-    },
     Model {
         model: Option<String>,
     },
@@ -189,13 +180,6 @@ impl SlashCommand {
             "help" => Self::Help,
             "status" => Self::Status,
             "compact" => Self::Compact,
-            "thinking" => Self::Thinking {
-                enabled: match parts.next() {
-                    Some("on") => Some(true),
-                    Some("off") => Some(false),
-                    Some(_) | None => None,
-                },
-            },
             "model" => Self::Model {
                 model: parts.next().map(ToOwned::to_owned),
             },
@@ -295,7 +279,6 @@ pub fn handle_slash_command(
             session: session.clone(),
         }),
         SlashCommand::Status
-        | SlashCommand::Thinking { .. }
         | SlashCommand::Model { .. }
         | SlashCommand::Permissions { .. }
         | SlashCommand::Clear { .. }
@@ -324,22 +307,6 @@ mod tests {
     fn parses_supported_slash_commands() {
         assert_eq!(SlashCommand::parse("/help"), Some(SlashCommand::Help));
         assert_eq!(SlashCommand::parse(" /status "), Some(SlashCommand::Status));
-        assert_eq!(
-            SlashCommand::parse("/thinking on"),
-            Some(SlashCommand::Thinking {
-                enabled: Some(true),
-            })
-        );
-        assert_eq!(
-            SlashCommand::parse("/thinking off"),
-            Some(SlashCommand::Thinking {
-                enabled: Some(false),
-            })
-        );
-        assert_eq!(
-            SlashCommand::parse("/thinking"),
-            Some(SlashCommand::Thinking { enabled: None })
-        );
         assert_eq!(
             SlashCommand::parse("/model claude-opus"),
             Some(SlashCommand::Model {
@@ -407,7 +374,6 @@ mod tests {
         assert!(help.contains("/help"));
         assert!(help.contains("/status"));
         assert!(help.contains("/compact"));
-        assert!(help.contains("/thinking [on|off]"));
         assert!(help.contains("/model [model]"));
         assert!(help.contains("/permissions [read-only|workspace-write|danger-full-access]"));
         assert!(help.contains("/clear [--confirm]"));
@@ -420,7 +386,7 @@ mod tests {
         assert!(help.contains("/version"));
         assert!(help.contains("/export [file]"));
         assert!(help.contains("/session [list|switch <session-id>]"));
-        assert_eq!(slash_command_specs().len(), 16);
+        assert_eq!(slash_command_specs().len(), 15);
         assert_eq!(resume_supported_slash_commands().len(), 11);
     }
 
@@ -468,9 +434,6 @@ mod tests {
         let session = Session::new();
         assert!(handle_slash_command("/unknown", &session, CompactionConfig::default()).is_none());
         assert!(handle_slash_command("/status", &session, CompactionConfig::default()).is_none());
-        assert!(
-            handle_slash_command("/thinking on", &session, CompactionConfig::default()).is_none()
-        );
         assert!(
             handle_slash_command("/model claude", &session, CompactionConfig::default()).is_none()
         );

rust/crates/runtime/src/compact.rs

@@ -130,7 +130,7 @@ fn summarize_messages(messages: &[ConversationMessage]) -> String {
         .filter_map(|block| match block {
             ContentBlock::ToolUse { name, .. } => Some(name.as_str()),
             ContentBlock::ToolResult { tool_name, .. } => Some(tool_name.as_str()),
-            ContentBlock::Text { .. } | ContentBlock::Thinking { .. } => None,
+            ContentBlock::Text { .. } => None,
         })
         .collect::<Vec<_>>();
     tool_names.sort_unstable();
@@ -200,7 +200,6 @@ fn summarize_messages(messages: &[ConversationMessage]) -> String {
 fn summarize_block(block: &ContentBlock) -> String {
     let raw = match block {
         ContentBlock::Text { text } => text.clone(),
-        ContentBlock::Thinking { text, .. } => format!("thinking: {text}"),
         ContentBlock::ToolUse { name, input, .. } => format!("tool_use {name}({input})"),
         ContentBlock::ToolResult {
             tool_name,
@@ -259,7 +258,7 @@ fn collect_key_files(messages: &[ConversationMessage]) -> Vec<String> {
         .iter()
         .flat_map(|message| message.blocks.iter())
         .map(|block| match block {
-            ContentBlock::Text { text } | ContentBlock::Thinking { text, .. } => text.as_str(),
+            ContentBlock::Text { text } => text.as_str(),
             ContentBlock::ToolUse { input, .. } => input.as_str(),
             ContentBlock::ToolResult { output, .. } => output.as_str(),
         })
@@ -281,15 +280,10 @@ fn infer_current_work(messages: &[ConversationMessage]) -> Option<String> {
 
 fn first_text_block(message: &ConversationMessage) -> Option<&str> {
     message.blocks.iter().find_map(|block| match block {
-        ContentBlock::Text { text } | ContentBlock::Thinking { text, .. }
-            if !text.trim().is_empty() =>
-        {
-            Some(text.as_str())
-        }
+        ContentBlock::Text { text } if !text.trim().is_empty() => Some(text.as_str()),
         ContentBlock::ToolUse { .. }
         | ContentBlock::ToolResult { .. }
-        | ContentBlock::Text { .. }
-        | ContentBlock::Thinking { .. } => None,
+        | ContentBlock::Text { .. } => None,
     })
 }
 
@@ -334,7 +328,7 @@ fn estimate_message_tokens(message: &ConversationMessage) -> usize {
         .blocks
         .iter()
         .map(|block| match block {
-            ContentBlock::Text { text } | ContentBlock::Thinking { text, .. } => text.len() / 4 + 1,
+            ContentBlock::Text { text } => text.len() / 4 + 1,
             ContentBlock::ToolUse { name, input, .. } => (name.len() + input.len()) / 4 + 1,
             ContentBlock::ToolResult {
                 tool_name, output, ..

rust/crates/runtime/src/conversation.rs

@@ -17,8 +17,6 @@ pub struct ApiRequest {
 #[derive(Debug, Clone, PartialEq, Eq)]
 pub enum AssistantEvent {
     TextDelta(String),
-    ThinkingDelta(String),
-    ThinkingSignature(String),
     ToolUse {
         id: String,
         name: String,
@@ -249,26 +247,15 @@ fn build_assistant_message(
     events: Vec<AssistantEvent>,
 ) -> Result<(ConversationMessage, Option<TokenUsage>), RuntimeError> {
     let mut text = String::new();
-    let mut thinking = String::new();
-    let mut thinking_signature: Option<String> = None;
     let mut blocks = Vec::new();
     let mut finished = false;
     let mut usage = None;
 
     for event in events {
         match event {
-            AssistantEvent::TextDelta(delta) => {
-                flush_thinking_block(&mut thinking, &mut thinking_signature, &mut blocks);
-                text.push_str(&delta);
-            }
-            AssistantEvent::ThinkingDelta(delta) => {
-                flush_text_block(&mut text, &mut blocks);
-                thinking.push_str(&delta);
-            }
-            AssistantEvent::ThinkingSignature(signature) => thinking_signature = Some(signature),
+            AssistantEvent::TextDelta(delta) => text.push_str(&delta),
             AssistantEvent::ToolUse { id, name, input } => {
                 flush_text_block(&mut text, &mut blocks);
-                flush_thinking_block(&mut thinking, &mut thinking_signature, &mut blocks);
                 blocks.push(ContentBlock::ToolUse { id, name, input });
             }
             AssistantEvent::Usage(value) => usage = Some(value),
@@ -279,7 +266,6 @@ fn build_assistant_message(
     }
 
     flush_text_block(&mut text, &mut blocks);
-    flush_thinking_block(&mut thinking, &mut thinking_signature, &mut blocks);
 
     if !finished {
         return Err(RuntimeError::new(
@@ -304,19 +290,6 @@ fn flush_text_block(text: &mut String, blocks: &mut Vec<ContentBlock>) {
     }
 }
 
-fn flush_thinking_block(
-    thinking: &mut String,
-    signature: &mut Option<String>,
-    blocks: &mut Vec<ContentBlock>,
-) {
-    if !thinking.is_empty() || signature.is_some() {
-        blocks.push(ContentBlock::Thinking {
-            text: std::mem::take(thinking),
-            signature: signature.take(),
-        });
-    }
-}
-
 type ToolHandler = Box<dyn FnMut(&str) -> Result<String, ToolError>>;
 
 #[derive(Default)]
@@ -352,8 +325,8 @@ impl ToolExecutor for StaticToolExecutor {
 #[cfg(test)]
 mod tests {
     use super::{
-        build_assistant_message, ApiClient, ApiRequest, AssistantEvent, ConversationRuntime,
-        RuntimeError, StaticToolExecutor,
+        ApiClient, ApiRequest, AssistantEvent, ConversationRuntime, RuntimeError,
+        StaticToolExecutor,
     };
     use crate::compact::CompactionConfig;
     use crate::permissions::{
@@ -529,29 +502,6 @@ mod tests {
         ));
     }
 
-    #[test]
-    fn thinking_blocks_are_preserved_separately_from_text() {
-        let (message, usage) = build_assistant_message(vec![
-            AssistantEvent::ThinkingDelta("first ".to_string()),
-            AssistantEvent::ThinkingDelta("second".to_string()),
-            AssistantEvent::ThinkingSignature("sig-1".to_string()),
-            AssistantEvent::TextDelta("final".to_string()),
-            AssistantEvent::MessageStop,
-        ])
-        .expect("assistant message should build");
-
-        assert_eq!(usage, None);
-        assert!(matches!(
-            &message.blocks[0],
-            ContentBlock::Thinking { text, signature }
-                if text == "first second" && signature.as_deref() == Some("sig-1")
-        ));
-        assert!(matches!(
-            &message.blocks[1],
-            ContentBlock::Text { text } if text == "final"
-        ));
-    }
-
     #[test]
     fn reconstructs_usage_tracker_from_restored_session() {
         struct SimpleApi;

rust/crates/runtime/src/session.rs

@@ -19,10 +19,6 @@ pub enum ContentBlock {
     Text {
         text: String,
     },
-    Thinking {
-        text: String,
-        signature: Option<String>,
-    },
     ToolUse {
         id: String,
         name: String,
@@ -261,19 +257,6 @@ impl ContentBlock {
                 object.insert("type".to_string(), JsonValue::String("text".to_string()));
                 object.insert("text".to_string(), JsonValue::String(text.clone()));
             }
-            Self::Thinking { text, signature } => {
-                object.insert(
-                    "type".to_string(),
-                    JsonValue::String("thinking".to_string()),
-                );
-                object.insert("text".to_string(), JsonValue::String(text.clone()));
-                if let Some(signature) = signature {
-                    object.insert(
-                        "signature".to_string(),
-                        JsonValue::String(signature.clone()),
-                    );
-                }
-            }
             Self::ToolUse { id, name, input } => {
                 object.insert(
                     "type".to_string(),
@@ -320,13 +303,6 @@ impl ContentBlock {
             "text" => Ok(Self::Text {
                 text: required_string(object, "text")?,
             }),
-            "thinking" => Ok(Self::Thinking {
-                text: required_string(object, "text")?,
-                signature: object
-                    .get("signature")
-                    .and_then(JsonValue::as_str)
-                    .map(ToOwned::to_owned),
-            }),
             "tool_use" => Ok(Self::ToolUse {
                 id: required_string(object, "id")?,
                 name: required_string(object, "name")?,