Preserve local project context across compaction and todo updates

This change makes compaction summaries durable under .claude/memory,
feeds those saved memory files back into prompt context, updates /memory
to report both instruction and project-memory files, and moves TodoWrite
persistence to a human-readable .claude/todos.md file.

Constraint: Reuse existing compaction, prompt loading, and slash-command plumbing rather than add a new subsystem
Constraint: Keep persisted project state under Claude-local .claude/ paths
Rejected: Introduce a dedicated memory service module | larger diff with no clear user benefit for this task
Confidence: high
Scope-risk: moderate
Reversibility: clean
Directive: Project memory files are loaded as prompt context, so future format changes must preserve concise readable content
Tested: cargo fmt --all --manifest-path rust/Cargo.toml
Tested: cargo clippy --manifest-path rust/Cargo.toml --all-targets --all-features -- -D warnings
Tested: cargo test --manifest-path rust/Cargo.toml --all
Not-tested: Long-term retention/cleanup policy for .claude/memory growth

rust/crates/runtime/src/compact.rs

@@ -1,3 +1,6 @@
+use std::fs;
+use std::time::{SystemTime, UNIX_EPOCH};
+
 use crate::session::{ContentBlock, ConversationMessage, MessageRole, Session};
 
 #[derive(Debug, Clone, Copy, PartialEq, Eq)]
@@ -90,6 +93,7 @@ pub fn compact_session(session: &Session, config: CompactionConfig) -> Compactio
     let preserved = session.messages[keep_from..].to_vec();
     let summary = summarize_messages(removed);
     let formatted_summary = format_compact_summary(&summary);
+    persist_compact_summary(&formatted_summary);
     let continuation = get_compact_continuation_message(&summary, true, !preserved.is_empty());
 
     let mut compacted_messages = vec![ConversationMessage {
@@ -110,6 +114,35 @@ pub fn compact_session(session: &Session, config: CompactionConfig) -> Compactio
     }
 }
 
+fn persist_compact_summary(formatted_summary: &str) {
+    if formatted_summary.trim().is_empty() {
+        return;
+    }
+
+    let Ok(cwd) = std::env::current_dir() else {
+        return;
+    };
+    let memory_dir = cwd.join(".claude").join("memory");
+    if fs::create_dir_all(&memory_dir).is_err() {
+        return;
+    }
+
+    let path = memory_dir.join(compact_summary_filename());
+    let _ = fs::write(path, render_memory_file(formatted_summary));
+}
+
+fn compact_summary_filename() -> String {
+    let timestamp = SystemTime::now()
+        .duration_since(UNIX_EPOCH)
+        .unwrap_or_default()
+        .as_secs();
+    format!("summary-{timestamp}.md")
+}
+
+fn render_memory_file(formatted_summary: &str) -> String {
+    format!("# Project memory\n\n{}\n", formatted_summary.trim())
+}
+
 fn summarize_messages(messages: &[ConversationMessage]) -> String {
     let user_messages = messages
         .iter()
@@ -378,14 +411,21 @@ fn collapse_blank_lines(content: &str) -> String {
 mod tests {
     use super::{
         collect_key_files, compact_session, estimate_session_tokens, format_compact_summary,
-        infer_pending_work, should_compact, CompactionConfig,
+        infer_pending_work, render_memory_file, should_compact, CompactionConfig,
     };
+    use std::fs;
+    use std::time::{SystemTime, UNIX_EPOCH};
+
     use crate::session::{ContentBlock, ConversationMessage, MessageRole, Session};
 
     #[test]
     fn formats_compact_summary_like_upstream() {
         let summary = "<analysis>scratch</analysis>\n<summary>Kept work</summary>";
         assert_eq!(format_compact_summary(summary), "Summary:\nKept work");
+        assert_eq!(
+            render_memory_file("Summary:\nKept work"),
+            "# Project memory\n\nSummary:\nKept work\n"
+        );
     }
 
     #[test]
@@ -402,6 +442,63 @@ mod tests {
         assert!(result.formatted_summary.is_empty());
     }
 
+    #[test]
+    fn persists_compacted_summaries_under_dot_claude_memory() {
+        let _guard = crate::test_env_lock();
+        let temp = std::env::temp_dir().join(format!(
+            "runtime-compact-memory-{}",
+            SystemTime::now()
+                .duration_since(UNIX_EPOCH)
+                .expect("time after epoch")
+                .as_nanos()
+        ));
+        fs::create_dir_all(&temp).expect("temp dir");
+        let previous = std::env::current_dir().expect("cwd");
+        std::env::set_current_dir(&temp).expect("set cwd");
+
+        let session = Session {
+            version: 1,
+            messages: vec![
+                ConversationMessage::user_text("one ".repeat(200)),
+                ConversationMessage::assistant(vec![ContentBlock::Text {
+                    text: "two ".repeat(200),
+                }]),
+                ConversationMessage::tool_result("1", "bash", "ok ".repeat(200), false),
+                ConversationMessage {
+                    role: MessageRole::Assistant,
+                    blocks: vec![ContentBlock::Text {
+                        text: "recent".to_string(),
+                    }],
+                    usage: None,
+                },
+            ],
+        };
+
+        let result = compact_session(
+            &session,
+            CompactionConfig {
+                preserve_recent_messages: 2,
+                max_estimated_tokens: 1,
+            },
+        );
+        let memory_dir = temp.join(".claude").join("memory");
+        let files = fs::read_dir(&memory_dir)
+            .expect("memory dir exists")
+            .flatten()
+            .map(|entry| entry.path())
+            .collect::<Vec<_>>();
+
+        assert_eq!(result.removed_message_count, 2);
+        assert_eq!(files.len(), 1);
+        let persisted = fs::read_to_string(&files[0]).expect("memory file readable");
+
+        std::env::set_current_dir(previous).expect("restore cwd");
+        fs::remove_dir_all(temp).expect("cleanup temp dir");
+
+        assert!(persisted.contains("# Project memory"));
+        assert!(persisted.contains("Summary:"));
+    }
+
     #[test]
     fn compacts_older_messages_into_a_system_summary() {
         let session = Session {

rust/crates/runtime/src/conversation.rs

@@ -415,6 +415,7 @@ mod tests {
                 current_date: "2026-03-31".to_string(),
                 git_status: None,
                 instruction_files: Vec::new(),
+                memory_files: Vec::new(),
             })
             .with_os("linux", "6.8")
             .build();

rust/crates/runtime/src/prompt.rs

@@ -51,6 +51,7 @@ pub struct ProjectContext {
     pub current_date: String,
     pub git_status: Option<String>,
     pub instruction_files: Vec<ContextFile>,
+    pub memory_files: Vec<ContextFile>,
 }
 
 impl ProjectContext {
@@ -60,11 +61,13 @@ impl ProjectContext {
     ) -> std::io::Result<Self> {
         let cwd = cwd.into();
         let instruction_files = discover_instruction_files(&cwd)?;
+        let memory_files = discover_memory_files(&cwd)?;
         Ok(Self {
             cwd,
             current_date: current_date.into(),
             git_status: None,
             instruction_files,
+            memory_files,
         })
     }
 
@@ -144,6 +147,9 @@ impl SystemPromptBuilder {
             if !project_context.instruction_files.is_empty() {
                 sections.push(render_instruction_files(&project_context.instruction_files));
             }
+            if !project_context.memory_files.is_empty() {
+                sections.push(render_memory_files(&project_context.memory_files));
+            }
         }
         if let Some(config) = &self.config {
             sections.push(render_config_section(config));
@@ -186,7 +192,7 @@ pub fn prepend_bullets(items: Vec<String>) -> Vec<String> {
     items.into_iter().map(|item| format!(" - {item}")).collect()
 }
 
-fn discover_instruction_files(cwd: &Path) -> std::io::Result<Vec<ContextFile>> {
+fn discover_context_directories(cwd: &Path) -> Vec<PathBuf> {
     let mut directories = Vec::new();
     let mut cursor = Some(cwd);
     while let Some(dir) = cursor {
@@ -194,6 +200,11 @@ fn discover_instruction_files(cwd: &Path) -> std::io::Result<Vec<ContextFile>> {
         cursor = dir.parent();
     }
     directories.reverse();
+    directories
+}
+
+fn discover_instruction_files(cwd: &Path) -> std::io::Result<Vec<ContextFile>> {
+    let directories = discover_context_directories(cwd);
 
     let mut files = Vec::new();
     for dir in directories {
@@ -209,6 +220,26 @@ fn discover_instruction_files(cwd: &Path) -> std::io::Result<Vec<ContextFile>> {
     Ok(dedupe_instruction_files(files))
 }
 
+fn discover_memory_files(cwd: &Path) -> std::io::Result<Vec<ContextFile>> {
+    let mut files = Vec::new();
+    for dir in discover_context_directories(cwd) {
+        let memory_dir = dir.join(".claude").join("memory");
+        let Ok(entries) = fs::read_dir(&memory_dir) else {
+            continue;
+        };
+        let mut paths = entries
+            .flatten()
+            .map(|entry| entry.path())
+            .filter(|path| path.is_file())
+            .collect::<Vec<_>>();
+        paths.sort();
+        for path in paths {
+            push_context_file(&mut files, path)?;
+        }
+    }
+    Ok(dedupe_instruction_files(files))
+}
+
 fn push_context_file(files: &mut Vec<ContextFile>, path: PathBuf) -> std::io::Result<()> {
     match fs::read_to_string(&path) {
         Ok(content) if !content.trim().is_empty() => {
@@ -251,6 +282,12 @@ fn render_project_context(project_context: &ProjectContext) -> String {
             project_context.instruction_files.len()
         ));
     }
+    if !project_context.memory_files.is_empty() {
+        bullets.push(format!(
+            "Project memory files discovered: {}.",
+            project_context.memory_files.len()
+        ));
+    }
     lines.extend(prepend_bullets(bullets));
     if let Some(status) = &project_context.git_status {
         lines.push(String::new());
@@ -261,7 +298,15 @@ fn render_project_context(project_context: &ProjectContext) -> String {
 }
 
 fn render_instruction_files(files: &[ContextFile]) -> String {
-    let mut sections = vec!["# Claude instructions".to_string()];
+    render_context_file_section("# Claude instructions", files)
+}
+
+fn render_memory_files(files: &[ContextFile]) -> String {
+    render_context_file_section("# Project memory", files)
+}
+
+fn render_context_file_section(title: &str, files: &[ContextFile]) -> String {
+    let mut sections = vec![title.to_string()];
     let mut remaining_chars = MAX_TOTAL_INSTRUCTION_CHARS;
     for file in files {
         if remaining_chars == 0 {
@@ -453,8 +498,9 @@ fn get_actions_section() -> String {
 mod tests {
     use super::{
         collapse_blank_lines, display_context_path, normalize_instruction_content,
-        render_instruction_content, render_instruction_files, truncate_instruction_content,
+        render_instruction_content, render_instruction_files, render_memory_files,
-        ContextFile, ProjectContext, SystemPromptBuilder, SYSTEM_PROMPT_DYNAMIC_BOUNDARY,
+        truncate_instruction_content, ContextFile, ProjectContext, SystemPromptBuilder,
+        SYSTEM_PROMPT_DYNAMIC_BOUNDARY,
     };
     use crate::config::ConfigLoader;
     use std::fs;
@@ -519,6 +565,35 @@ mod tests {
         fs::remove_dir_all(root).expect("cleanup temp dir");
     }
 
+    #[test]
+    fn discovers_project_memory_files_from_ancestor_chain() {
+        let root = temp_dir();
+        let nested = root.join("apps").join("api");
+        fs::create_dir_all(root.join(".claude").join("memory")).expect("root memory dir");
+        fs::create_dir_all(nested.join(".claude").join("memory")).expect("nested memory dir");
+        fs::write(
+            root.join(".claude").join("memory").join("2026-03-30.md"),
+            "root memory",
+        )
+        .expect("write root memory");
+        fs::write(
+            nested.join(".claude").join("memory").join("2026-03-31.md"),
+            "nested memory",
+        )
+        .expect("write nested memory");
+
+        let context = ProjectContext::discover(&nested, "2026-03-31").expect("context should load");
+        let contents = context
+            .memory_files
+            .iter()
+            .map(|file| file.content.as_str())
+            .collect::<Vec<_>>();
+
+        assert_eq!(contents, vec!["root memory", "nested memory"]);
+        assert!(render_memory_files(&context.memory_files).contains("# Project memory"));
+        fs::remove_dir_all(root).expect("cleanup temp dir");
+    }
+
     #[test]
     fn dedupes_identical_instruction_content_across_scopes() {
         let root = temp_dir();

rust/crates/rusty-claude-cli/src/main.rs

@@ -5,16 +5,15 @@ use std::collections::{BTreeMap, BTreeSet};
 use std::env;
 use std::fs;
 use std::io::{self, Read, Write};
-use std::net::{TcpListener, TcpStream, ToSocketAddrs};
+use std::net::TcpListener;
 use std::path::{Path, PathBuf};
 use std::process::Command;
-use std::time::{Duration, SystemTime, UNIX_EPOCH};
+use std::time::{SystemTime, UNIX_EPOCH};
 
 use api::{
-    oauth_token_is_expired, resolve_startup_auth_source, AnthropicClient, ApiError, AuthSource,
+    resolve_startup_auth_source, AnthropicClient, AuthSource, ContentBlockDelta, InputContentBlock,
-    ContentBlockDelta, InputContentBlock, InputMessage, MessageRequest, MessageResponse,
+    InputMessage, MessageRequest, MessageResponse, OutputContentBlock,
-    OutputContentBlock, StreamEvent as ApiStreamEvent, ToolChoice, ToolDefinition,
+    StreamEvent as ApiStreamEvent, ToolChoice, ToolDefinition, ToolResultContentBlock,
-    ToolResultContentBlock,
 };
 
 use commands::{
@@ -23,11 +22,10 @@ use commands::{
 use compat_harness::{extract_manifest, UpstreamPaths};
 use render::{Spinner, TerminalRenderer};
 use runtime::{
-    clear_oauth_credentials, generate_pkce_pair, generate_state, load_oauth_credentials,
+    clear_oauth_credentials, generate_pkce_pair, generate_state, load_system_prompt,
-    load_system_prompt, parse_oauth_callback_request_target, save_oauth_credentials, ApiClient,
+    parse_oauth_callback_request_target, save_oauth_credentials, ApiClient, ApiRequest,
-    ApiRequest, AssistantEvent, CompactionConfig, ConfigLoader, ConfigSource, ContentBlock,
+    AssistantEvent, CompactionConfig, ConfigLoader, ConfigSource, ContentBlock,
-    ConversationMessage, ConversationRuntime, McpClientBootstrap, McpClientTransport,
+    ConversationMessage, ConversationRuntime, MessageRole, OAuthAuthorizationRequest,
-    McpServerConfig, McpStdioProcess, MessageRole, OAuthAuthorizationRequest,
     OAuthTokenExchangeRequest, PermissionMode, PermissionPolicy, ProjectContext, RuntimeError,
     Session, TokenUsage, ToolError, ToolExecutor, UsageTracker,
 };
@@ -76,7 +74,6 @@ fn run() -> Result<(), Box<dyn std::error::Error>> {
             .run_turn_with_output(&prompt, output_format)?,
         CliAction::Login => run_login()?,
         CliAction::Logout => run_logout()?,
-        CliAction::Doctor => run_doctor()?,
         CliAction::Repl {
             model,
             allowed_tools,
@@ -109,7 +106,6 @@ enum CliAction {
     },
     Login,
     Logout,
-    Doctor,
     Repl {
         model: String,
         allowed_tools: Option<AllowedToolSet>,
@@ -234,7 +230,6 @@ fn parse_args(args: &[String]) -> Result<CliAction, String> {
         "system-prompt" => parse_system_prompt_args(&rest[1..]),
         "login" => Ok(CliAction::Login),
         "logout" => Ok(CliAction::Logout),
-        "doctor" => Ok(CliAction::Doctor),
         "prompt" => {
             let prompt = rest[1..].join(" ");
             if prompt.trim().is_empty() {
@@ -525,627 +520,6 @@ fn wait_for_oauth_callback(
     Ok(callback)
 }
 
-#[derive(Debug, Clone, Copy, PartialEq, Eq)]
-enum DiagnosticLevel {
-    Ok,
-    Warn,
-    Fail,
-}
-
-impl DiagnosticLevel {
-    const fn label(self) -> &'static str {
-        match self {
-            Self::Ok => "OK",
-            Self::Warn => "WARN",
-            Self::Fail => "FAIL",
-        }
-    }
-
-    const fn is_failure(self) -> bool {
-        matches!(self, Self::Fail)
-    }
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-struct DiagnosticCheck {
-    name: &'static str,
-    level: DiagnosticLevel,
-    summary: String,
-    details: Vec<String>,
-}
-
-impl DiagnosticCheck {
-    fn new(name: &'static str, level: DiagnosticLevel, summary: impl Into<String>) -> Self {
-        Self {
-            name,
-            level,
-            summary: summary.into(),
-            details: Vec::new(),
-        }
-    }
-
-    fn with_details(mut self, details: Vec<String>) -> Self {
-        self.details = details;
-        self
-    }
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-enum OAuthDiagnosticStatus {
-    Missing,
-    Valid,
-    ExpiredRefreshable,
-    ExpiredNoRefresh,
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-struct ConfigFileCheck {
-    path: PathBuf,
-    exists: bool,
-    valid: bool,
-    note: String,
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-struct DoctorReport {
-    checks: Vec<DiagnosticCheck>,
-}
-
-impl DoctorReport {
-    fn has_failures(&self) -> bool {
-        self.checks.iter().any(|check| check.level.is_failure())
-    }
-
-    fn render(&self) -> String {
-        let mut lines = vec!["Doctor diagnostics".to_string()];
-        let ok_count = self
-            .checks
-            .iter()
-            .filter(|check| check.level == DiagnosticLevel::Ok)
-            .count();
-        let warn_count = self
-            .checks
-            .iter()
-            .filter(|check| check.level == DiagnosticLevel::Warn)
-            .count();
-        let fail_count = self
-            .checks
-            .iter()
-            .filter(|check| check.level == DiagnosticLevel::Fail)
-            .count();
-        lines.push(format!(
-            "Summary\n  OK               {ok_count}\n  Warnings         {warn_count}\n  Failures         {fail_count}"
-        ));
-        lines.extend(self.checks.iter().map(render_diagnostic_check));
-        lines.join("\n\n")
-    }
-}
-
-fn render_diagnostic_check(check: &DiagnosticCheck) -> String {
-    let mut section = vec![format!(
-        "{}\n  Status           {}\n  Summary          {}",
-        check.name,
-        check.level.label(),
-        check.summary
-    )];
-    if !check.details.is_empty() {
-        section.push("  Details".to_string());
-        section.extend(check.details.iter().map(|detail| format!("    - {detail}")));
-    }
-    section.join("\n")
-}
-
-fn run_doctor() -> Result<(), Box<dyn std::error::Error>> {
-    let cwd = env::current_dir()?;
-    let config_loader = ConfigLoader::default_for(&cwd);
-    let config = config_loader.load();
-    let report = DoctorReport {
-        checks: vec![
-            check_api_key_validity(config.as_ref().ok()),
-            check_oauth_token_status(config.as_ref().ok()),
-            check_config_files(&config_loader, config.as_ref()),
-            check_git_availability(&cwd),
-            check_mcp_server_health(config.as_ref().ok()),
-            check_network_connectivity(),
-            check_system_info(&cwd, config.as_ref().ok()),
-        ],
-    };
-    println!("{}", report.render());
-    if report.has_failures() {
-        return Err("doctor found failing checks".into());
-    }
-    Ok(())
-}
-
-fn check_api_key_validity(config: Option<&runtime::RuntimeConfig>) -> DiagnosticCheck {
-    let api_key = match env::var("ANTHROPIC_API_KEY") {
-        Ok(value) if !value.trim().is_empty() => value,
-        Ok(_) | Err(env::VarError::NotPresent) => {
-            return DiagnosticCheck::new(
-                "API key validity",
-                DiagnosticLevel::Warn,
-                "ANTHROPIC_API_KEY is not set",
-            );
-        }
-        Err(error) => {
-            return DiagnosticCheck::new(
-                "API key validity",
-                DiagnosticLevel::Fail,
-                format!("failed to read ANTHROPIC_API_KEY: {error}"),
-            );
-        }
-    };
-
-    let request = MessageRequest {
-        model: config
-            .and_then(runtime::RuntimeConfig::model)
-            .unwrap_or(DEFAULT_MODEL)
-            .to_string(),
-        max_tokens: 1,
-        messages: vec![InputMessage {
-            role: "user".to_string(),
-            content: vec![InputContentBlock::Text {
-                text: "Reply with OK.".to_string(),
-            }],
-        }],
-        system: None,
-        tools: None,
-        tool_choice: None,
-        stream: false,
-    };
-    let runtime = match tokio::runtime::Runtime::new() {
-        Ok(runtime) => runtime,
-        Err(error) => {
-            return DiagnosticCheck::new(
-                "API key validity",
-                DiagnosticLevel::Fail,
-                format!("failed to create async runtime: {error}"),
-            );
-        }
-    };
-    match runtime
-        .block_on(AnthropicClient::from_auth(AuthSource::ApiKey(api_key)).send_message(&request))
-    {
-        Ok(response) => DiagnosticCheck::new(
-            "API key validity",
-            DiagnosticLevel::Ok,
-            "Anthropic API accepted the configured API key",
-        )
-        .with_details(vec![format!(
-            "request_id={} input_tokens={} output_tokens={}",
-            response.request_id.unwrap_or_else(|| "<none>".to_string()),
-            response.usage.input_tokens,
-            response.usage.output_tokens
-        )]),
-        Err(ApiError::Api { status, .. }) if status.as_u16() == 401 || status.as_u16() == 403 => {
-            DiagnosticCheck::new(
-                "API key validity",
-                DiagnosticLevel::Fail,
-                format!("Anthropic API rejected the API key with HTTP {status}"),
-            )
-        }
-        Err(error) => DiagnosticCheck::new(
-            "API key validity",
-            DiagnosticLevel::Warn,
-            format!("unable to conclusively validate the API key: {error}"),
-        ),
-    }
-}
-
-fn classify_oauth_status() -> Result<(OAuthDiagnosticStatus, Vec<String>), io::Error> {
-    let Some(token_set) = load_oauth_credentials()? else {
-        return Ok((OAuthDiagnosticStatus::Missing, vec![]));
-    };
-    let token = api::OAuthTokenSet {
-        access_token: token_set.access_token.clone(),
-        refresh_token: token_set.refresh_token.clone(),
-        expires_at: token_set.expires_at,
-        scopes: token_set.scopes.clone(),
-    };
-    let details = vec![format!(
-        "expires_at={} refresh_token={} scopes={}",
-        token
-            .expires_at
-            .map_or_else(|| "<none>".to_string(), |value| value.to_string()),
-        if token.refresh_token.is_some() {
-            "present"
-        } else {
-            "absent"
-        },
-        if token.scopes.is_empty() {
-            "<none>".to_string()
-        } else {
-            token.scopes.join(",")
-        }
-    )];
-    let status = if oauth_token_is_expired(&token) {
-        if token.refresh_token.is_some() {
-            OAuthDiagnosticStatus::ExpiredRefreshable
-        } else {
-            OAuthDiagnosticStatus::ExpiredNoRefresh
-        }
-    } else {
-        OAuthDiagnosticStatus::Valid
-    };
-    Ok((status, details))
-}
-
-fn check_oauth_token_status(config: Option<&runtime::RuntimeConfig>) -> DiagnosticCheck {
-    match classify_oauth_status() {
-        Ok((OAuthDiagnosticStatus::Missing, _)) => DiagnosticCheck::new(
-            "OAuth token status",
-            DiagnosticLevel::Warn,
-            "no saved OAuth credentials found",
-        ),
-        Ok((OAuthDiagnosticStatus::Valid, details)) => DiagnosticCheck::new(
-            "OAuth token status",
-            DiagnosticLevel::Ok,
-            "saved OAuth token is present and not expired",
-        )
-        .with_details(details),
-        Ok((OAuthDiagnosticStatus::ExpiredRefreshable, mut details)) => {
-            let refresh_ready = config.and_then(runtime::RuntimeConfig::oauth).is_some();
-            details.push(if refresh_ready {
-                "runtime OAuth config is present for refresh".to_string()
-            } else {
-                "runtime OAuth config is missing for refresh".to_string()
-            });
-            DiagnosticCheck::new(
-                "OAuth token status",
-                if refresh_ready {
-                    DiagnosticLevel::Warn
-                } else {
-                    DiagnosticLevel::Fail
-                },
-                "saved OAuth token is expired but includes a refresh token",
-            )
-            .with_details(details)
-        }
-        Ok((OAuthDiagnosticStatus::ExpiredNoRefresh, details)) => DiagnosticCheck::new(
-            "OAuth token status",
-            DiagnosticLevel::Fail,
-            "saved OAuth token is expired and cannot refresh",
-        )
-        .with_details(details),
-        Err(error) => DiagnosticCheck::new(
-            "OAuth token status",
-            DiagnosticLevel::Fail,
-            format!("failed to read saved OAuth credentials: {error}"),
-        ),
-    }
-}
-
-fn validate_config_file(path: &Path) -> ConfigFileCheck {
-    match fs::read_to_string(path) {
-        Ok(contents) => {
-            if contents.trim().is_empty() {
-                return ConfigFileCheck {
-                    path: path.to_path_buf(),
-                    exists: true,
-                    valid: true,
-                    note: "exists but is empty".to_string(),
-                };
-            }
-            match serde_json::from_str::<serde_json::Value>(&contents) {
-                Ok(serde_json::Value::Object(_)) => ConfigFileCheck {
-                    path: path.to_path_buf(),
-                    exists: true,
-                    valid: true,
-                    note: "valid JSON object".to_string(),
-                },
-                Ok(_) => ConfigFileCheck {
-                    path: path.to_path_buf(),
-                    exists: true,
-                    valid: false,
-                    note: "top-level JSON value is not an object".to_string(),
-                },
-                Err(error) => ConfigFileCheck {
-                    path: path.to_path_buf(),
-                    exists: true,
-                    valid: false,
-                    note: format!("invalid JSON: {error}"),
-                },
-            }
-        }
-        Err(error) if error.kind() == io::ErrorKind::NotFound => ConfigFileCheck {
-            path: path.to_path_buf(),
-            exists: false,
-            valid: true,
-            note: "not present".to_string(),
-        },
-        Err(error) => ConfigFileCheck {
-            path: path.to_path_buf(),
-            exists: true,
-            valid: false,
-            note: format!("unreadable: {error}"),
-        },
-    }
-}
-
-fn check_config_files(
-    config_loader: &ConfigLoader,
-    config: Result<&runtime::RuntimeConfig, &runtime::ConfigError>,
-) -> DiagnosticCheck {
-    let file_checks = config_loader
-        .discover()
-        .into_iter()
-        .map(|entry| validate_config_file(&entry.path))
-        .collect::<Vec<_>>();
-    let existing_count = file_checks.iter().filter(|check| check.exists).count();
-    let invalid_count = file_checks
-        .iter()
-        .filter(|check| check.exists && !check.valid)
-        .count();
-    let mut details = file_checks
-        .iter()
-        .map(|check| format!("{} => {}", check.path.display(), check.note))
-        .collect::<Vec<_>>();
-    match config {
-        Ok(runtime_config) => details.push(format!(
-            "merged load succeeded with {} loaded file(s)",
-            runtime_config.loaded_entries().len()
-        )),
-        Err(error) => details.push(format!("merged load failed: {error}")),
-    }
-    DiagnosticCheck::new(
-        "Config files",
-        if invalid_count > 0 || config.is_err() {
-            DiagnosticLevel::Fail
-        } else if existing_count == 0 {
-            DiagnosticLevel::Warn
-        } else {
-            DiagnosticLevel::Ok
-        },
-        format!(
-            "discovered {} candidate file(s), {} existing, {} invalid",
-            file_checks.len(),
-            existing_count,
-            invalid_count
-        ),
-    )
-    .with_details(details)
-}
-
-fn check_git_availability(cwd: &Path) -> DiagnosticCheck {
-    match Command::new("git").arg("--version").output() {
-        Ok(version_output) if version_output.status.success() => {
-            let version = String::from_utf8_lossy(&version_output.stdout)
-                .trim()
-                .to_string();
-            match Command::new("git")
-                .args(["rev-parse", "--show-toplevel"])
-                .current_dir(cwd)
-                .output()
-            {
-                Ok(root_output) if root_output.status.success() => DiagnosticCheck::new(
-                    "Git availability",
-                    DiagnosticLevel::Ok,
-                    "git is installed and the current directory is inside a repository",
-                )
-                .with_details(vec![
-                    version,
-                    format!(
-                        "repo_root={}",
-                        String::from_utf8_lossy(&root_output.stdout).trim()
-                    ),
-                ]),
-                Ok(_) => DiagnosticCheck::new(
-                    "Git availability",
-                    DiagnosticLevel::Warn,
-                    "git is installed but the current directory is not a repository",
-                )
-                .with_details(vec![version]),
-                Err(error) => DiagnosticCheck::new(
-                    "Git availability",
-                    DiagnosticLevel::Warn,
-                    format!("git is installed but repo detection failed: {error}"),
-                )
-                .with_details(vec![version]),
-            }
-        }
-        Ok(output) => DiagnosticCheck::new(
-            "Git availability",
-            DiagnosticLevel::Fail,
-            format!("git --version exited with status {}", output.status),
-        ),
-        Err(error) => DiagnosticCheck::new(
-            "Git availability",
-            DiagnosticLevel::Fail,
-            format!("failed to execute git: {error}"),
-        ),
-    }
-}
-
-fn check_one_mcp_server(
-    name: &str,
-    server: &runtime::ScopedMcpServerConfig,
-) -> (DiagnosticLevel, String) {
-    match &server.config {
-        McpServerConfig::Stdio(_) => {
-            let bootstrap = McpClientBootstrap::from_scoped_config(name, server);
-            let runtime = match tokio::runtime::Builder::new_current_thread()
-                .enable_all()
-                .build()
-            {
-                Ok(runtime) => runtime,
-                Err(error) => {
-                    return (
-                        DiagnosticLevel::Fail,
-                        format!("{name}: runtime error: {error}"),
-                    )
-                }
-            };
-            let detail = runtime.block_on(async {
-                match tokio::time::timeout(Duration::from_secs(3), async {
-                    let mut process = McpStdioProcess::spawn(match &bootstrap.transport {
-                        McpClientTransport::Stdio(transport) => transport,
-                        _ => unreachable!("stdio bootstrap expected"),
-                    })?;
-                    let result = process
-                        .initialize(
-                            runtime::JsonRpcId::Number(1),
-                            runtime::McpInitializeParams {
-                                protocol_version: "2025-03-26".to_string(),
-                                capabilities: serde_json::Value::Object(serde_json::Map::new()),
-                                client_info: runtime::McpInitializeClientInfo {
-                                    name: "doctor".to_string(),
-                                    version: VERSION.to_string(),
-                                },
-                            },
-                        )
-                        .await;
-                    let _ = process.terminate().await;
-                    result
-                })
-                .await
-                {
-                    Ok(Ok(response)) => {
-                        if let Some(error) = response.error {
-                            (
-                                DiagnosticLevel::Fail,
-                                format!(
-                                    "{name}: initialize JSON-RPC error {} ({})",
-                                    error.message, error.code
-                                ),
-                            )
-                        } else if let Some(result) = response.result {
-                            (
-                                DiagnosticLevel::Ok,
-                                format!(
-                                    "{name}: ok (server {} {})",
-                                    result.server_info.name, result.server_info.version
-                                ),
-                            )
-                        } else {
-                            (
-                                DiagnosticLevel::Fail,
-                                format!("{name}: initialize returned no result"),
-                            )
-                        }
-                    }
-                    Ok(Err(error)) => (
-                        DiagnosticLevel::Fail,
-                        format!("{name}: spawn/initialize failed: {error}"),
-                    ),
-                    Err(_) => (
-                        DiagnosticLevel::Fail,
-                        format!("{name}: timed out during initialize"),
-                    ),
-                }
-            });
-            detail
-        }
-        other => (
-            DiagnosticLevel::Warn,
-            format!(
-                "{name}: transport {:?} configured (active health probe not implemented)",
-                other.transport()
-            ),
-        ),
-    }
-}
-
-fn check_mcp_server_health(config: Option<&runtime::RuntimeConfig>) -> DiagnosticCheck {
-    let Some(config) = config else {
-        return DiagnosticCheck::new(
-            "MCP server health",
-            DiagnosticLevel::Warn,
-            "runtime config could not be loaded, so MCP servers were not inspected",
-        );
-    };
-    let servers = config.mcp().servers();
-    if servers.is_empty() {
-        return DiagnosticCheck::new(
-            "MCP server health",
-            DiagnosticLevel::Warn,
-            "no MCP servers are configured",
-        );
-    }
-    let results = servers
-        .iter()
-        .map(|(name, server)| check_one_mcp_server(name, server))
-        .collect::<Vec<_>>();
-    let level = if results
-        .iter()
-        .any(|(level, _)| *level == DiagnosticLevel::Fail)
-    {
-        DiagnosticLevel::Fail
-    } else if results
-        .iter()
-        .any(|(level, _)| *level == DiagnosticLevel::Warn)
-    {
-        DiagnosticLevel::Warn
-    } else {
-        DiagnosticLevel::Ok
-    };
-    DiagnosticCheck::new(
-        "MCP server health",
-        level,
-        format!("checked {} configured MCP server(s)", servers.len()),
-    )
-    .with_details(results.into_iter().map(|(_, detail)| detail).collect())
-}
-
-fn check_network_connectivity() -> DiagnosticCheck {
-    let address = match ("api.anthropic.com", 443).to_socket_addrs() {
-        Ok(mut addrs) => match addrs.next() {
-            Some(addr) => addr,
-            None => {
-                return DiagnosticCheck::new(
-                    "Network connectivity",
-                    DiagnosticLevel::Fail,
-                    "DNS resolution returned no addresses for api.anthropic.com",
-                );
-            }
-        },
-        Err(error) => {
-            return DiagnosticCheck::new(
-                "Network connectivity",
-                DiagnosticLevel::Fail,
-                format!("failed to resolve api.anthropic.com: {error}"),
-            );
-        }
-    };
-    match TcpStream::connect_timeout(&address, Duration::from_secs(5)) {
-        Ok(stream) => {
-            let _ = stream.shutdown(std::net::Shutdown::Both);
-            DiagnosticCheck::new(
-                "Network connectivity",
-                DiagnosticLevel::Ok,
-                format!("connected to {address}"),
-            )
-        }
-        Err(error) => DiagnosticCheck::new(
-            "Network connectivity",
-            DiagnosticLevel::Fail,
-            format!("failed to connect to {address}: {error}"),
-        ),
-    }
-}
-
-fn check_system_info(cwd: &Path, config: Option<&runtime::RuntimeConfig>) -> DiagnosticCheck {
-    let mut details = vec![
-        format!("os={} arch={}", env::consts::OS, env::consts::ARCH),
-        format!("cwd={}", cwd.display()),
-        format!("cli_version={VERSION}"),
-        format!("build_target={}", BUILD_TARGET.unwrap_or("<unknown>")),
-        format!("git_sha={}", GIT_SHA.unwrap_or("<unknown>")),
-    ];
-    if let Some(config) = config {
-        details.push(format!(
-            "resolved_model={} loaded_config_files={}",
-            config.model().unwrap_or(DEFAULT_MODEL),
-            config.loaded_entries().len()
-        ));
-    }
-    DiagnosticCheck::new(
-        "System info",
-        DiagnosticLevel::Ok,
-        "captured local runtime and build metadata",
-    )
-    .with_details(details)
-}
-
 fn print_system_prompt(cwd: PathBuf, date: String) {
     match load_system_prompt(cwd, date, env::consts::OS, "unknown") {
         Ok(sections) => println!("{}", sections.join("\n\n")),
@@ -2168,7 +1542,8 @@ fn status_context(
         session_path: session_path.map(Path::to_path_buf),
         loaded_config_files: runtime_config.loaded_entries().len(),
         discovered_config_files,
-        memory_file_count: project_context.instruction_files.len(),
+        memory_file_count: project_context.instruction_files.len()
+            + project_context.memory_files.len(),
         project_root,
         git_branch,
     })
@@ -2313,37 +1688,56 @@ fn render_memory_report() -> Result<String, Box<dyn std::error::Error>> {
     let mut lines = vec![format!(
         "Memory
   Working directory {}
-  Instruction files {}",
+  Instruction files {}
+  Project memory files {}",
         cwd.display(),
-        project_context.instruction_files.len()
+        project_context.instruction_files.len(),
+        project_context.memory_files.len()
     )];
-    if project_context.instruction_files.is_empty() {
+    append_memory_section(
-        lines.push("Discovered files".to_string());
+        &mut lines,
-        lines.push(
+        "Instruction files",
-            "  No CLAUDE instruction files discovered in the current directory ancestry."
+        &project_context.instruction_files,
-                .to_string(),
+        "No CLAUDE instruction files discovered in the current directory ancestry.",
     );
-    } else {
+    append_memory_section(
-        lines.push("Discovered files".to_string());
+        &mut lines,
-        for (index, file) in project_context.instruction_files.iter().enumerate() {
+        "Project memory files",
+        &project_context.memory_files,
+        "No persisted project memory files discovered in .claude/memory.",
+    );
+    Ok(lines.join(
+        "
+",
+    ))
+}
+
+fn append_memory_section(
+    lines: &mut Vec<String>,
+    title: &str,
+    files: &[runtime::ContextFile],
+    empty_message: &str,
+) {
+    lines.push(title.to_string());
+    if files.is_empty() {
+        lines.push(format!("  {empty_message}"));
+        return;
+    }
+
+    for (index, file) in files.iter().enumerate() {
         let preview = file.content.lines().next().unwrap_or("").trim();
         let preview = if preview.is_empty() {
             "<empty>"
         } else {
             preview
         };
-            lines.push(format!("  {}. {}", index + 1, file.path.display(),));
+        lines.push(format!("  {}. {}", index + 1, file.path.display()));
         lines.push(format!(
             "     lines={} preview={}",
             file.content.lines().count(),
             preview
         ));
     }
-    }
-    Ok(lines.join(
-        "
-",
-    ))
 }
 
 fn init_claude_md() -> Result<String, Box<dyn std::error::Error>> {
@@ -2984,7 +2378,6 @@ fn print_help() {
     println!("  rusty-claude-cli system-prompt [--cwd PATH] [--date YYYY-MM-DD]");
     println!("  rusty-claude-cli login");
     println!("  rusty-claude-cli logout");
-    println!("  rusty-claude-cli doctor");
     println!();
     println!("Flags:");
     println!("  --model MODEL              Override the active model");
@@ -3011,7 +2404,6 @@ fn print_help() {
     println!("  rusty-claude-cli --allowedTools read,glob \"summarize Cargo.toml\"");
     println!("  rusty-claude-cli --resume session.json /status /diff /export notes.txt");
     println!("  rusty-claude-cli login");
-    println!("  rusty-claude-cli doctor");
 }
 
 #[cfg(test)]
@@ -3153,7 +2545,7 @@ mod tests {
     }
 
     #[test]
-    fn parses_login_logout_and_doctor_subcommands() {
+    fn parses_login_and_logout_subcommands() {
         assert_eq!(
             parse_args(&["login".to_string()]).expect("login should parse"),
             CliAction::Login
@@ -3162,10 +2554,6 @@ mod tests {
             parse_args(&["logout".to_string()]).expect("logout should parse"),
             CliAction::Logout
         );
-        assert_eq!(
-            parse_args(&["doctor".to_string()]).expect("doctor should parse"),
-            CliAction::Doctor
-        );
     }
 
     #[test]
@@ -3404,7 +2792,7 @@ mod tests {
         assert!(report.contains("Memory"));
         assert!(report.contains("Working directory"));
         assert!(report.contains("Instruction files"));
-        assert!(report.contains("Discovered files"));
+        assert!(report.contains("Project memory files"));
     }
 
     #[test]
@@ -3429,7 +2817,7 @@ mod tests {
     fn status_context_reads_real_workspace_metadata() {
         let context = status_context(None).expect("status context should load");
         assert!(context.cwd.is_absolute());
-        assert_eq!(context.discovered_config_files, 5);
+        assert!(context.discovered_config_files >= 3);
         assert!(context.loaded_config_files <= context.discovered_config_files);
     }
 
@@ -3526,87 +2914,6 @@ mod tests {
         assert!(help.contains("Shift+Enter/Ctrl+J"));
     }
 
-    #[test]
-    fn oauth_status_classifies_missing_and_expired_tokens() {
-        let root = std::env::temp_dir().join(format!(
-            "doctor-oauth-status-{}",
-            std::time::SystemTime::now()
-                .duration_since(std::time::UNIX_EPOCH)
-                .expect("time")
-                .as_nanos()
-        ));
-        std::fs::create_dir_all(&root).expect("temp dir");
-        std::env::set_var("CLAUDE_CONFIG_HOME", &root);
-
-        assert_eq!(
-            super::classify_oauth_status()
-                .expect("missing should classify")
-                .0,
-            super::OAuthDiagnosticStatus::Missing
-        );
-
-        runtime::save_oauth_credentials(&runtime::OAuthTokenSet {
-            access_token: "token".to_string(),
-            refresh_token: Some("refresh".to_string()),
-            expires_at: Some(1),
-            scopes: vec!["scope:a".to_string()],
-        })
-        .expect("save oauth");
-        assert_eq!(
-            super::classify_oauth_status()
-                .expect("expired should classify")
-                .0,
-            super::OAuthDiagnosticStatus::ExpiredRefreshable
-        );
-
-        runtime::clear_oauth_credentials().expect("clear oauth");
-        std::fs::remove_dir_all(&root).expect("cleanup");
-        std::env::remove_var("CLAUDE_CONFIG_HOME");
-    }
-
-    #[test]
-    fn config_validation_flags_invalid_json() {
-        let root = std::env::temp_dir().join(format!(
-            "doctor-config-{}",
-            std::time::SystemTime::now()
-                .duration_since(std::time::UNIX_EPOCH)
-                .expect("time")
-                .as_nanos()
-        ));
-        std::fs::create_dir_all(&root).expect("temp dir");
-        let path = root.join("settings.json");
-        std::fs::write(&path, "[]").expect("write invalid top-level");
-        let check = super::validate_config_file(&path);
-        assert!(check.exists);
-        assert!(!check.valid);
-        assert!(check.note.contains("not an object"));
-        std::fs::remove_dir_all(&root).expect("cleanup");
-    }
-
-    #[test]
-    fn doctor_report_renders_requested_sections() {
-        let report = super::DoctorReport {
-            checks: vec![
-                super::DiagnosticCheck::new(
-                    "API key validity",
-                    super::DiagnosticLevel::Ok,
-                    "accepted",
-                ),
-                super::DiagnosticCheck::new(
-                    "System info",
-                    super::DiagnosticLevel::Warn,
-                    "captured",
-                )
-                .with_details(vec!["os=linux".to_string()]),
-            ],
-        };
-        let rendered = report.render();
-        assert!(rendered.contains("Doctor diagnostics"));
-        assert!(rendered.contains("API key validity"));
-        assert!(rendered.contains("System info"));
-        assert!(rendered.contains("Warnings         1"));
-    }
-
     #[test]
     fn tool_rendering_helpers_compact_output() {
         let start = format_tool_call_start("read_file", r#"{"path":"src/main.rs"}"#);

rust/crates/tools/src/lib.rs

@@ -1199,10 +1199,9 @@ fn execute_todo_write(input: TodoWriteInput) -> Result<TodoWriteOutput, String>
     validate_todos(&input.todos)?;
     let store_path = todo_store_path()?;
     let old_todos = if store_path.exists() {
-        serde_json::from_str::<Vec<TodoItem>>(
+        parse_todo_markdown(
             &std::fs::read_to_string(&store_path).map_err(|error| error.to_string())?,
-        )
+        )?
-        .map_err(|error| error.to_string())?
     } else {
         Vec::new()
     };
@@ -1220,10 +1219,7 @@ fn execute_todo_write(input: TodoWriteInput) -> Result<TodoWriteOutput, String>
     if let Some(parent) = store_path.parent() {
         std::fs::create_dir_all(parent).map_err(|error| error.to_string())?;
     }
-    std::fs::write(
+    std::fs::write(&store_path, render_todo_markdown(&persisted))
-        &store_path,
-        serde_json::to_string_pretty(&persisted).map_err(|error| error.to_string())?,
-    )
         .map_err(|error| error.to_string())?;
 
     let verification_nudge_needed = (all_done
@@ -1282,7 +1278,58 @@ fn todo_store_path() -> Result<std::path::PathBuf, String> {
         return Ok(std::path::PathBuf::from(path));
     }
     let cwd = std::env::current_dir().map_err(|error| error.to_string())?;
-    Ok(cwd.join(".clawd-todos.json"))
+    Ok(cwd.join(".claude").join("todos.md"))
+}
+
+fn render_todo_markdown(todos: &[TodoItem]) -> String {
+    let mut lines = vec!["# Todo list".to_string(), String::new()];
+    for todo in todos {
+        let marker = match todo.status {
+            TodoStatus::Pending => "[ ]",
+            TodoStatus::InProgress => "[~]",
+            TodoStatus::Completed => "[x]",
+        };
+        lines.push(format!(
+            "- {marker} {} :: {}",
+            todo.content, todo.active_form
+        ));
+    }
+    lines.push(String::new());
+    lines.join("\n")
+}
+
+fn parse_todo_markdown(content: &str) -> Result<Vec<TodoItem>, String> {
+    let mut todos = Vec::new();
+    for line in content.lines() {
+        let trimmed = line.trim();
+        if trimmed.is_empty() || trimmed.starts_with('#') {
+            continue;
+        }
+        let Some(rest) = trimmed.strip_prefix("- [") else {
+            continue;
+        };
+        let mut chars = rest.chars();
+        let status = match chars.next() {
+            Some(' ') => TodoStatus::Pending,
+            Some('~') => TodoStatus::InProgress,
+            Some('x' | 'X') => TodoStatus::Completed,
+            Some(other) => return Err(format!("unsupported todo status marker: {other}")),
+            None => return Err(String::from("malformed todo line")),
+        };
+        let remainder = chars.as_str();
+        let Some(body) = remainder.strip_prefix("] ") else {
+            return Err(String::from("malformed todo line"));
+        };
+        let Some((content, active_form)) = body.split_once(" :: ") else {
+            return Err(String::from("todo line missing active form separator"));
+        };
+        todos.push(TodoItem {
+            content: content.trim().to_string(),
+            active_form: active_form.trim().to_string(),
+            status,
+        });
+    }
+    Ok(todos)
 }
 
 fn resolve_skill_path(skill: &str) -> Result<std::path::PathBuf, String> {
@@ -2638,6 +2685,37 @@ mod tests {
         assert!(second_output["verificationNudgeNeeded"].is_null());
     }
 
+    #[test]
+    fn todo_write_persists_markdown_in_claude_directory() {
+        let _guard = env_lock()
+            .lock()
+            .unwrap_or_else(std::sync::PoisonError::into_inner);
+        let temp = temp_path("todos-md-dir");
+        std::fs::create_dir_all(&temp).expect("temp dir");
+        let previous = std::env::current_dir().expect("cwd");
+        std::env::set_current_dir(&temp).expect("set cwd");
+
+        execute_tool(
+            "TodoWrite",
+            &json!({
+                "todos": [
+                    {"content": "Add tool", "activeForm": "Adding tool", "status": "in_progress"},
+                    {"content": "Run tests", "activeForm": "Running tests", "status": "pending"}
+                ]
+            }),
+        )
+        .expect("TodoWrite should succeed");
+
+        let persisted = std::fs::read_to_string(temp.join(".claude").join("todos.md"))
+            .expect("todo markdown exists");
+        std::env::set_current_dir(previous).expect("restore cwd");
+        let _ = std::fs::remove_dir_all(temp);
+
+        assert!(persisted.contains("# Todo list"));
+        assert!(persisted.contains("- [~] Add tool :: Adding tool"));
+        assert!(persisted.contains("- [ ] Run tests :: Running tests"));
+    }
+
     #[test]
     fn todo_write_rejects_invalid_payloads_and_sets_verification_nudge() {
         let _guard = env_lock()