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/Cargo.lock

@@ -1091,11 +1091,8 @@ dependencies = [
  "compat-harness",
  "crossterm",
  "pulldown-cmark",
- "reqwest",
  "runtime",
- "serde",
  "serde_json",
- "sha2",
  "syntect",
  "tokio",
  "tools",

rust/README.md

@@ -84,15 +84,6 @@ cargo run -p rusty-claude-cli -- logout
 
 This removes only the stored OAuth credentials and preserves unrelated JSON fields in `credentials.json`.
 
-### Self-update
-
-```bash
-cd rust
-cargo run -p rusty-claude-cli -- self-update
-```
-
-The command checks the latest GitHub release for `instructkr/clawd-code`, compares it to the current binary version, downloads the matching binary asset plus checksum manifest, verifies SHA-256, replaces the current executable, and prints the release changelog. If no published release or matching asset exists, it exits safely with an explanatory message.
-
 ## Usage examples
 
 ### 1) Prompt mode
@@ -171,7 +162,6 @@ cargo run -p rusty-claude-cli -- --resume session.json /memory /config
 - `dump-manifests` — print extracted upstream manifest counts
 - `bootstrap-plan` — print the current bootstrap skeleton
 - `system-prompt [--cwd PATH] [--date YYYY-MM-DD]` — render the synthesized system prompt
-- `self-update` — update the installed binary from the latest GitHub release when a matching asset is available
 - `--help` / `-h` — show CLI help
 - `--version` / `-V` — print the CLI version and build info locally (no API call)
 - `--output-format text|json` — choose non-interactive prompt output rendering

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/Cargo.toml

@@ -11,11 +11,8 @@ commands = { path = "../commands" }
 compat-harness = { path = "../compat-harness" }
 crossterm = "0.28"
 pulldown-cmark = "0.13"
-reqwest = { version = "0.12", default-features = false, features = ["blocking", "json", "rustls-tls"] }
 runtime = { path = "../runtime" }
-serde = { version = "1", features = ["derive"] }
 serde_json = "1"
-sha2 = "0.10"
 syntect = "5"
 tokio = { version = "1", features = ["rt-multi-thread", "time"] }
 tools = { path = "../tools" }

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

@@ -3,7 +3,6 @@ mod render;
 
 use std::collections::{BTreeMap, BTreeSet};
 use std::env;
-use std::fmt::Write as _;
 use std::fs;
 use std::io::{self, Read, Write};
 use std::net::TcpListener;
@@ -22,7 +21,6 @@ use commands::{
 };
 use compat_harness::{extract_manifest, UpstreamPaths};
 use render::{Spinner, TerminalRenderer};
-use reqwest::blocking::Client;
 use runtime::{
     clear_oauth_credentials, generate_pkce_pair, generate_state, load_system_prompt,
     parse_oauth_callback_request_target, save_oauth_credentials, ApiClient, ApiRequest,
@@ -31,9 +29,7 @@ use runtime::{
     OAuthTokenExchangeRequest, PermissionMode, PermissionPolicy, ProjectContext, RuntimeError,
     Session, TokenUsage, ToolError, ToolExecutor, UsageTracker,
 };
-use serde::Deserialize;
 use serde_json::json;
-use sha2::{Digest, Sha256};
 use tools::{execute_tool, mvp_tool_specs, ToolSpec};
 
 const DEFAULT_MODEL: &str = "claude-sonnet-4-20250514";
@@ -43,18 +39,6 @@ const DEFAULT_OAUTH_CALLBACK_PORT: u16 = 4545;
 const VERSION: &str = env!("CARGO_PKG_VERSION");
 const BUILD_TARGET: Option<&str> = option_env!("TARGET");
 const GIT_SHA: Option<&str> = option_env!("GIT_SHA");
-const SELF_UPDATE_REPOSITORY: &str = "instructkr/clawd-code";
-const SELF_UPDATE_LATEST_RELEASE_URL: &str =
-    "https://api.github.com/repos/instructkr/clawd-code/releases/latest";
-const SELF_UPDATE_USER_AGENT: &str = "rusty-claude-cli-self-update";
-const CHECKSUM_ASSET_CANDIDATES: &[&str] = &[
-    "SHA256SUMS",
-    "SHA256SUMS.txt",
-    "sha256sums",
-    "sha256sums.txt",
-    "checksums.txt",
-    "checksums.sha256",
-];
 
 type AllowedToolSet = BTreeSet<String>;
 
@@ -76,7 +60,6 @@ fn run() -> Result<(), Box<dyn std::error::Error>> {
         CliAction::BootstrapPlan => print_bootstrap_plan(),
         CliAction::PrintSystemPrompt { cwd, date } => print_system_prompt(cwd, date),
         CliAction::Version => print_version(),
-        CliAction::SelfUpdate => run_self_update()?,
         CliAction::ResumeSession {
             session_path,
             commands,
@@ -110,7 +93,6 @@ enum CliAction {
         date: String,
     },
     Version,
-    SelfUpdate,
     ResumeSession {
         session_path: PathBuf,
         commands: Vec<String>,
@@ -246,7 +228,6 @@ fn parse_args(args: &[String]) -> Result<CliAction, String> {
         "dump-manifests" => Ok(CliAction::DumpManifests),
         "bootstrap-plan" => Ok(CliAction::BootstrapPlan),
         "system-prompt" => parse_system_prompt_args(&rest[1..]),
-        "self-update" => Ok(CliAction::SelfUpdate),
         "login" => Ok(CliAction::Login),
         "logout" => Ok(CliAction::Logout),
         "prompt" => {
@@ -553,375 +534,6 @@ fn print_version() {
     println!("{}", render_version_report());
 }
 
-#[derive(Debug, Clone, Deserialize, PartialEq, Eq)]
-struct GitHubRelease {
-    tag_name: String,
-    #[serde(default)]
-    body: String,
-    #[serde(default)]
-    assets: Vec<GitHubReleaseAsset>,
-}
-
-#[derive(Debug, Clone, Deserialize, PartialEq, Eq)]
-struct GitHubReleaseAsset {
-    name: String,
-    browser_download_url: String,
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-struct SelectedReleaseAssets {
-    binary: GitHubReleaseAsset,
-    checksum: GitHubReleaseAsset,
-}
-
-fn run_self_update() -> Result<(), Box<dyn std::error::Error>> {
-    let Some(release) = fetch_latest_release()? else {
-        println!(
-            "{}",
-            render_update_report(
-                "No published release available",
-                Some(VERSION),
-                None,
-                Some("GitHub latest release endpoint returned no published release for instructkr/clawd-code."),
-                None,
-            )
-        );
-        return Ok(());
-    };
-
-    let latest_version = normalize_version_tag(&release.tag_name);
-    if !is_newer_version(VERSION, &latest_version) {
-        println!(
-            "{}",
-            render_update_report(
-                "Already up to date",
-                Some(VERSION),
-                Some(&latest_version),
-                Some("Current binary already matches the latest published release."),
-                Some(&release.body),
-            )
-        );
-        return Ok(());
-    }
-
-    let selected = match select_release_assets(&release) {
-        Ok(selected) => selected,
-        Err(message) => {
-            println!(
-                "{}",
-                render_update_report(
-                    "Release found, but no installable asset matched this platform",
-                    Some(VERSION),
-                    Some(&latest_version),
-                    Some(&message),
-                    Some(&release.body),
-                )
-            );
-            return Ok(());
-        }
-    };
-
-    let client = build_self_update_client()?;
-    let binary_bytes = download_bytes(&client, &selected.binary.browser_download_url)?;
-    let checksum_manifest = download_text(&client, &selected.checksum.browser_download_url)?;
-    let expected_checksum = parse_checksum_for_asset(&checksum_manifest, &selected.binary.name)
-        .ok_or_else(|| {
-            format!(
-                "checksum manifest did not contain an entry for {}",
-                selected.binary.name
-            )
-        })?;
-    let actual_checksum = sha256_hex(&binary_bytes);
-    if actual_checksum != expected_checksum {
-        return Err(format!(
-            "downloaded asset checksum mismatch for {} (expected {}, got {})",
-            selected.binary.name, expected_checksum, actual_checksum
-        )
-        .into());
-    }
-
-    replace_current_executable(&binary_bytes)?;
-
-    println!(
-        "{}",
-        render_update_report(
-            "Update installed",
-            Some(VERSION),
-            Some(&latest_version),
-            Some(&format!(
-                "Installed {} from GitHub release assets for {}.",
-                selected.binary.name,
-                current_target()
-            )),
-            Some(&release.body),
-        )
-    );
-    Ok(())
-}
-
-fn fetch_latest_release() -> Result<Option<GitHubRelease>, Box<dyn std::error::Error>> {
-    let client = build_self_update_client()?;
-    let response = client
-        .get(SELF_UPDATE_LATEST_RELEASE_URL)
-        .header(reqwest::header::ACCEPT, "application/vnd.github+json")
-        .send()?;
-
-    if response.status() == reqwest::StatusCode::NOT_FOUND {
-        return Ok(None);
-    }
-
-    let response = response.error_for_status()?;
-    Ok(Some(response.json()?))
-}
-
-fn build_self_update_client() -> Result<Client, reqwest::Error> {
-    Client::builder().user_agent(SELF_UPDATE_USER_AGENT).build()
-}
-
-fn download_bytes(client: &Client, url: &str) -> Result<Vec<u8>, Box<dyn std::error::Error>> {
-    let response = client.get(url).send()?.error_for_status()?;
-    Ok(response.bytes()?.to_vec())
-}
-
-fn download_text(client: &Client, url: &str) -> Result<String, Box<dyn std::error::Error>> {
-    let response = client.get(url).send()?.error_for_status()?;
-    Ok(response.text()?)
-}
-
-fn normalize_version_tag(version: &str) -> String {
-    version.trim().trim_start_matches('v').to_string()
-}
-
-fn is_newer_version(current: &str, latest: &str) -> bool {
-    compare_versions(latest, current).is_gt()
-}
-
-fn current_target() -> String {
-    BUILD_TARGET.map_or_else(default_target_triple, str::to_string)
-}
-
-fn release_asset_candidates() -> Vec<String> {
-    let mut candidates = target_name_candidates()
-        .into_iter()
-        .flat_map(|target| {
-            let mut names = vec![format!("rusty-claude-cli-{target}")];
-            if env::consts::OS == "windows" {
-                names.push(format!("rusty-claude-cli-{target}.exe"));
-            }
-            names
-        })
-        .collect::<Vec<_>>();
-    if env::consts::OS == "windows" {
-        candidates.push("rusty-claude-cli.exe".to_string());
-    }
-    candidates.push("rusty-claude-cli".to_string());
-    candidates.sort();
-    candidates.dedup();
-    candidates
-}
-
-fn select_release_assets(release: &GitHubRelease) -> Result<SelectedReleaseAssets, String> {
-    let binary = release_asset_candidates()
-        .into_iter()
-        .find_map(|candidate| {
-            release
-                .assets
-                .iter()
-                .find(|asset| asset.name == candidate)
-                .cloned()
-        })
-        .ok_or_else(|| {
-            format!(
-                "no binary asset matched target {} (expected one of: {})",
-                current_target(),
-                release_asset_candidates().join(", ")
-            )
-        })?;
-
-    let checksum = CHECKSUM_ASSET_CANDIDATES
-        .iter()
-        .find_map(|candidate| {
-            release
-                .assets
-                .iter()
-                .find(|asset| asset.name == *candidate)
-                .cloned()
-        })
-        .ok_or_else(|| {
-            format!(
-                "release did not include a checksum manifest (expected one of: {})",
-                CHECKSUM_ASSET_CANDIDATES.join(", ")
-            )
-        })?;
-
-    Ok(SelectedReleaseAssets { binary, checksum })
-}
-
-fn parse_checksum_for_asset(manifest: &str, asset_name: &str) -> Option<String> {
-    manifest.lines().find_map(|line| {
-        let trimmed = line.trim();
-        if trimmed.is_empty() {
-            return None;
-        }
-        if let Some((left, right)) = trimmed.split_once(" = ") {
-            return left
-                .strip_prefix("SHA256 (")
-                .and_then(|value| value.strip_suffix(')'))
-                .filter(|file| *file == asset_name)
-                .map(|_| right.to_ascii_lowercase());
-        }
-        let mut parts = trimmed.split_whitespace();
-        let checksum = parts.next()?;
-        let file = parts
-            .next_back()
-            .or_else(|| parts.next())?
-            .trim_start_matches('*');
-        (file == asset_name).then(|| checksum.to_ascii_lowercase())
-    })
-}
-
-fn sha256_hex(bytes: &[u8]) -> String {
-    format!("{:x}", Sha256::digest(bytes))
-}
-
-fn replace_current_executable(binary_bytes: &[u8]) -> Result<(), Box<dyn std::error::Error>> {
-    let current = env::current_exe()?;
-    replace_executable_at(&current, binary_bytes)
-}
-
-fn replace_executable_at(
-    current: &Path,
-    binary_bytes: &[u8],
-) -> Result<(), Box<dyn std::error::Error>> {
-    let temp_path = current.with_extension("download");
-    let backup_path = current.with_extension("bak");
-
-    if backup_path.exists() {
-        fs::remove_file(&backup_path)?;
-    }
-    fs::write(&temp_path, binary_bytes)?;
-    copy_executable_permissions(current, &temp_path)?;
-
-    fs::rename(current, &backup_path)?;
-    if let Err(error) = fs::rename(&temp_path, current) {
-        let _ = fs::rename(&backup_path, current);
-        let _ = fs::remove_file(&temp_path);
-        return Err(format!("failed to replace current executable: {error}").into());
-    }
-
-    if let Err(error) = fs::remove_file(&backup_path) {
-        eprintln!(
-            "warning: failed to remove self-update backup {}: {error}",
-            backup_path.display()
-        );
-    }
-    Ok(())
-}
-
-#[cfg(unix)]
-fn copy_executable_permissions(
-    source: &Path,
-    destination: &Path,
-) -> Result<(), Box<dyn std::error::Error>> {
-    use std::os::unix::fs::PermissionsExt;
-
-    let mode = fs::metadata(source)?.permissions().mode();
-    fs::set_permissions(destination, fs::Permissions::from_mode(mode))?;
-    Ok(())
-}
-
-#[cfg(not(unix))]
-fn copy_executable_permissions(
-    _source: &Path,
-    _destination: &Path,
-) -> Result<(), Box<dyn std::error::Error>> {
-    Ok(())
-}
-
-fn render_update_report(
-    result: &str,
-    current_version: Option<&str>,
-    latest_version: Option<&str>,
-    detail: Option<&str>,
-    changelog: Option<&str>,
-) -> String {
-    let mut report = String::from(
-        "Self-update
-",
-    );
-    let _ = writeln!(report, "  Repository       {SELF_UPDATE_REPOSITORY}");
-    let _ = writeln!(report, "  Result           {result}");
-    if let Some(current_version) = current_version {
-        let _ = writeln!(report, "  Current version  {current_version}");
-    }
-    if let Some(latest_version) = latest_version {
-        let _ = writeln!(report, "  Latest version   {latest_version}");
-    }
-    if let Some(detail) = detail {
-        let _ = writeln!(report, "  Detail           {detail}");
-    }
-    let trimmed = changelog.map(str::trim).filter(|value| !value.is_empty());
-    if let Some(changelog) = trimmed {
-        report.push_str(
-            "
-Changelog
-",
-        );
-        report.push_str(changelog);
-    }
-    report.trim_end().to_string()
-}
-
-fn compare_versions(left: &str, right: &str) -> std::cmp::Ordering {
-    let left = normalize_version_tag(left);
-    let right = normalize_version_tag(right);
-    let left_parts = version_components(&left);
-    let right_parts = version_components(&right);
-    let max_len = left_parts.len().max(right_parts.len());
-    for index in 0..max_len {
-        let left_part = *left_parts.get(index).unwrap_or(&0);
-        let right_part = *right_parts.get(index).unwrap_or(&0);
-        match left_part.cmp(&right_part) {
-            std::cmp::Ordering::Equal => {}
-            ordering => return ordering,
-        }
-    }
-    std::cmp::Ordering::Equal
-}
-
-fn version_components(version: &str) -> Vec<u64> {
-    version
-        .split(['.', '-'])
-        .map(|part| {
-            part.chars()
-                .take_while(char::is_ascii_digit)
-                .collect::<String>()
-        })
-        .filter(|part| !part.is_empty())
-        .filter_map(|part| part.parse::<u64>().ok())
-        .collect()
-}
-
-fn default_target_triple() -> String {
-    let os = match env::consts::OS {
-        "linux" => "unknown-linux-gnu",
-        "macos" => "apple-darwin",
-        "windows" => "pc-windows-msvc",
-        other => other,
-    };
-    format!("{}-{os}", env::consts::ARCH)
-}
-
-fn target_name_candidates() -> Vec<String> {
-    let mut candidates = Vec::new();
-    if let Some(target) = BUILD_TARGET {
-        candidates.push(target.to_string());
-    }
-    candidates.push(default_target_triple());
-    candidates.push(format!("{}-{}", env::consts::ARCH, env::consts::OS));
-    candidates
-}
-
 fn resume_session(session_path: &Path, commands: &[String]) {
     let session = match Session::load_from_path(session_path) {
         Ok(session) => session,
@@ -1930,7 +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,
     })
@@ -2075,39 +1688,58 @@ 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",
-            let preview = file.content.lines().next().unwrap_or("").trim();
+        &project_context.memory_files,
-            let preview = if preview.is_empty() {
+        "No persisted project memory files discovered in .claude/memory.",
-                "<empty>"
+    );
-            } else {
-                preview
-            };
-            lines.push(format!("  {}. {}", index + 1, file.path.display(),));
-            lines.push(format!(
-                "     lines={} preview={}",
-                file.content.lines().count(),
-                preview
-            ));
-        }
-    }
     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!(
+            "     lines={} preview={}",
+            file.content.lines().count(),
+            preview
+        ));
+    }
+}
+
 fn init_claude_md() -> Result<String, Box<dyn std::error::Error>> {
     let cwd = env::current_dir()?;
     let claude_md = cwd.join("CLAUDE.md");
@@ -2746,8 +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 self-update");
-    println!("      Update the installed binary from the latest GitHub release");
     println!();
     println!("Flags:");
     println!("  --model MODEL              Override the active model");
@@ -2774,7 +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 self-update");
 }
 
 #[cfg(test)]
@@ -2783,11 +2412,10 @@ mod tests {
         filter_tool_specs, format_compact_report, format_cost_report, format_init_report,
         format_model_report, format_model_switch_report, format_permissions_report,
         format_permissions_switch_report, format_resume_report, format_status_report,
-        format_tool_call_start, format_tool_result, is_newer_version, normalize_permission_mode,
+        format_tool_call_start, format_tool_result, normalize_permission_mode, parse_args,
-        normalize_version_tag, parse_args, parse_checksum_for_asset, parse_git_status_metadata,
+        parse_git_status_metadata, render_config_report, render_init_claude_md,
-        render_config_report, render_init_claude_md, render_memory_report, render_repl_help,
+        render_memory_report, render_repl_help, resume_supported_slash_commands, status_context,
-        render_update_report, resume_supported_slash_commands, select_release_assets,
+        CliAction, CliOutputFormat, SlashCommand, StatusUsage, DEFAULT_MODEL,
-        status_context, CliAction, CliOutputFormat, SlashCommand, StatusUsage, DEFAULT_MODEL,
     };
     use runtime::{ContentBlock, ConversationMessage, MessageRole, PermissionMode};
     use std::path::{Path, PathBuf};
@@ -2856,64 +2484,6 @@ mod tests {
         );
     }
 
-    #[test]
-    fn parses_self_update_subcommand() {
-        assert_eq!(
-            parse_args(&["self-update".to_string()]).expect("self-update should parse"),
-            CliAction::SelfUpdate
-        );
-    }
-
-    #[test]
-    fn normalize_version_tag_trims_v_prefix() {
-        assert_eq!(normalize_version_tag("v0.1.0"), "0.1.0");
-        assert_eq!(normalize_version_tag("0.1.0"), "0.1.0");
-    }
-
-    #[test]
-    fn detects_when_latest_version_differs() {
-        assert!(!is_newer_version("0.1.0", "v0.1.0"));
-        assert!(is_newer_version("0.1.0", "v0.2.0"));
-    }
-
-    #[test]
-    fn parses_checksum_manifest_for_named_asset() {
-        let manifest = "abc123 *rusty-claude-cli\ndef456  other-file\n";
-        assert_eq!(
-            parse_checksum_for_asset(manifest, "rusty-claude-cli"),
-            Some("abc123".to_string())
-        );
-    }
-
-    #[test]
-    fn select_release_assets_requires_checksum_file() {
-        let release = super::GitHubRelease {
-            tag_name: "v0.2.0".to_string(),
-            body: String::new(),
-            assets: vec![super::GitHubReleaseAsset {
-                name: "rusty-claude-cli".to_string(),
-                browser_download_url: "https://example.invalid/rusty-claude-cli".to_string(),
-            }],
-        };
-
-        let error = select_release_assets(&release).expect_err("missing checksum should error");
-        assert!(error.contains("checksum manifest"));
-    }
-
-    #[test]
-    fn update_report_includes_changelog_when_present() {
-        let report = render_update_report(
-            "Already up to date",
-            Some("0.1.0"),
-            Some("0.1.0"),
-            Some("No action taken."),
-            Some("- Added self-update"),
-        );
-        assert!(report.contains("Self-update"));
-        assert!(report.contains("Changelog"));
-        assert!(report.contains("- Added self-update"));
-    }
-
     #[test]
     fn parses_permission_mode_flag() {
         let args = vec!["--permission-mode=read-only".to_string()];
@@ -3222,7 +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]

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()
     };
@@ -1220,11 +1219,8 @@ 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,
+        .map_err(|error| error.to_string())?;
-        serde_json::to_string_pretty(&persisted).map_err(|error| error.to_string())?,
-    )
-    .map_err(|error| error.to_string())?;
 
     let verification_nudge_needed = (all_done
         && input.todos.len() >= 3
@@ -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()