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/commands/src/lib.rs

@@ -51,12 +51,6 @@ const SLASH_COMMAND_SPECS: &[SlashCommandSpec] = &[
         argument_hint: None,
         resume_supported: true,
     },
-    SlashCommandSpec {
-        name: "sandbox",
-        summary: "Show sandbox isolation status",
-        argument_hint: None,
-        resume_supported: true,
-    },
     SlashCommandSpec {
         name: "compact",
         summary: "Compact local session history",
@@ -141,7 +135,6 @@ const SLASH_COMMAND_SPECS: &[SlashCommandSpec] = &[
 pub enum SlashCommand {
     Help,
     Status,
-    Sandbox,
     Compact,
     Model {
         model: Option<String>,
@@ -186,7 +179,6 @@ impl SlashCommand {
         Some(match command {
             "help" => Self::Help,
             "status" => Self::Status,
-            "sandbox" => Self::Sandbox,
             "compact" => Self::Compact,
             "model" => Self::Model {
                 model: parts.next().map(ToOwned::to_owned),
@@ -287,7 +279,6 @@ pub fn handle_slash_command(
             session: session.clone(),
         }),
         SlashCommand::Status
-        | SlashCommand::Sandbox
         | SlashCommand::Model { .. }
         | SlashCommand::Permissions { .. }
         | SlashCommand::Clear { .. }
@@ -316,7 +307,6 @@ mod tests {
     fn parses_supported_slash_commands() {
         assert_eq!(SlashCommand::parse("/help"), Some(SlashCommand::Help));
         assert_eq!(SlashCommand::parse(" /status "), Some(SlashCommand::Status));
-        assert_eq!(SlashCommand::parse("/sandbox"), Some(SlashCommand::Sandbox));
         assert_eq!(
             SlashCommand::parse("/model claude-opus"),
             Some(SlashCommand::Model {
@@ -383,7 +373,6 @@ mod tests {
         assert!(help.contains("works with --resume SESSION.json"));
         assert!(help.contains("/help"));
         assert!(help.contains("/status"));
-        assert!(help.contains("/sandbox"));
         assert!(help.contains("/compact"));
         assert!(help.contains("/model [model]"));
         assert!(help.contains("/permissions [read-only|workspace-write|danger-full-access]"));
@@ -397,8 +386,8 @@ mod tests {
         assert!(help.contains("/version"));
         assert!(help.contains("/export [file]"));
         assert!(help.contains("/session [list|switch <session-id>]"));
-        assert_eq!(slash_command_specs().len(), 16);
-        assert_eq!(resume_supported_slash_commands().len(), 12);
+        assert_eq!(slash_command_specs().len(), 15);
+        assert_eq!(resume_supported_slash_commands().len(), 11);
     }
 
     #[test]
@@ -445,7 +434,6 @@ mod tests {
         let session = Session::new();
         assert!(handle_slash_command("/unknown", &session, CompactionConfig::default()).is_none());
         assert!(handle_slash_command("/status", &session, CompactionConfig::default()).is_none());
-        assert!(handle_slash_command("/sandbox", &session, CompactionConfig::default()).is_none());
         assert!(
             handle_slash_command("/model claude", &session, CompactionConfig::default()).is_none()
         );

rust/crates/runtime/src/bash.rs

@@ -1,4 +1,3 @@
-use std::env;
 use std::io;
 use std::process::{Command, Stdio};
 use std::time::Duration;
@@ -8,12 +7,6 @@ use tokio::process::Command as TokioCommand;
 use tokio::runtime::Builder;
 use tokio::time::timeout;
 
-use crate::sandbox::{
-    build_linux_sandbox_command, resolve_sandbox_status_for_request, FilesystemIsolationMode,
-    SandboxConfig, SandboxStatus,
-};
-use crate::ConfigLoader;
-
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Eq)]
 pub struct BashCommandInput {
     pub command: String,
@@ -23,14 +16,6 @@ pub struct BashCommandInput {
     pub run_in_background: Option<bool>,
     #[serde(rename = "dangerouslyDisableSandbox")]
     pub dangerously_disable_sandbox: Option<bool>,
-    #[serde(rename = "namespaceRestrictions")]
-    pub namespace_restrictions: Option<bool>,
-    #[serde(rename = "isolateNetwork")]
-    pub isolate_network: Option<bool>,
-    #[serde(rename = "filesystemMode")]
-    pub filesystem_mode: Option<FilesystemIsolationMode>,
-    #[serde(rename = "allowedMounts")]
-    pub allowed_mounts: Option<Vec<String>>,
 }
 
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
@@ -60,17 +45,13 @@ pub struct BashCommandOutput {
     pub persisted_output_path: Option<String>,
     #[serde(rename = "persistedOutputSize")]
     pub persisted_output_size: Option<u64>,
-    #[serde(rename = "sandboxStatus")]
-    pub sandbox_status: Option<SandboxStatus>,
 }
 
 pub fn execute_bash(input: BashCommandInput) -> io::Result<BashCommandOutput> {
-    let cwd = env::current_dir()?;
-    let sandbox_status = sandbox_status_for_input(&input, &cwd);
-
     if input.run_in_background.unwrap_or(false) {
-        let mut child = prepare_command(&input.command, &cwd, &sandbox_status, false);
-        let child = child
+        let child = Command::new("sh")
+            .arg("-lc")
+            .arg(&input.command)
             .stdin(Stdio::null())
             .stdout(Stdio::null())
             .stderr(Stdio::null())
@@ -91,20 +72,16 @@ pub fn execute_bash(input: BashCommandInput) -> io::Result<BashCommandOutput> {
             structured_content: None,
             persisted_output_path: None,
             persisted_output_size: None,
-            sandbox_status: Some(sandbox_status),
         });
     }
 
     let runtime = Builder::new_current_thread().enable_all().build()?;
-    runtime.block_on(execute_bash_async(input, sandbox_status, cwd))
+    runtime.block_on(execute_bash_async(input))
 }
 
-async fn execute_bash_async(
-    input: BashCommandInput,
-    sandbox_status: SandboxStatus,
-    cwd: std::path::PathBuf,
-) -> io::Result<BashCommandOutput> {
-    let mut command = prepare_tokio_command(&input.command, &cwd, &sandbox_status, true);
+async fn execute_bash_async(input: BashCommandInput) -> io::Result<BashCommandOutput> {
+    let mut command = TokioCommand::new("sh");
+    command.arg("-lc").arg(&input.command);
 
     let output_result = if let Some(timeout_ms) = input.timeout {
         match timeout(Duration::from_millis(timeout_ms), command.output()).await {
@@ -125,7 +102,6 @@ async fn execute_bash_async(
                     structured_content: None,
                     persisted_output_path: None,
                     persisted_output_size: None,
-                    sandbox_status: Some(sandbox_status),
                 });
             }
         }
@@ -160,88 +136,12 @@ async fn execute_bash_async(
         structured_content: None,
         persisted_output_path: None,
         persisted_output_size: None,
-        sandbox_status: Some(sandbox_status),
     })
 }
 
-fn sandbox_status_for_input(input: &BashCommandInput, cwd: &std::path::Path) -> SandboxStatus {
-    let config = ConfigLoader::default_for(cwd).load().map_or_else(
-        |_| SandboxConfig::default(),
-        |runtime_config| runtime_config.sandbox().clone(),
-    );
-    let request = config.resolve_request(
-        input.dangerously_disable_sandbox.map(|disabled| !disabled),
-        input.namespace_restrictions,
-        input.isolate_network,
-        input.filesystem_mode,
-        input.allowed_mounts.clone(),
-    );
-    resolve_sandbox_status_for_request(&request, cwd)
-}
-
-fn prepare_command(
-    command: &str,
-    cwd: &std::path::Path,
-    sandbox_status: &SandboxStatus,
-    create_dirs: bool,
-) -> Command {
-    if create_dirs {
-        prepare_sandbox_dirs(cwd);
-    }
-
-    if let Some(launcher) = build_linux_sandbox_command(command, cwd, sandbox_status) {
-        let mut prepared = Command::new(launcher.program);
-        prepared.args(launcher.args);
-        prepared.current_dir(cwd);
-        prepared.envs(launcher.env);
-        return prepared;
-    }
-
-    let mut prepared = Command::new("sh");
-    prepared.arg("-lc").arg(command).current_dir(cwd);
-    if sandbox_status.filesystem_active {
-        prepared.env("HOME", cwd.join(".sandbox-home"));
-        prepared.env("TMPDIR", cwd.join(".sandbox-tmp"));
-    }
-    prepared
-}
-
-fn prepare_tokio_command(
-    command: &str,
-    cwd: &std::path::Path,
-    sandbox_status: &SandboxStatus,
-    create_dirs: bool,
-) -> TokioCommand {
-    if create_dirs {
-        prepare_sandbox_dirs(cwd);
-    }
-
-    if let Some(launcher) = build_linux_sandbox_command(command, cwd, sandbox_status) {
-        let mut prepared = TokioCommand::new(launcher.program);
-        prepared.args(launcher.args);
-        prepared.current_dir(cwd);
-        prepared.envs(launcher.env);
-        return prepared;
-    }
-
-    let mut prepared = TokioCommand::new("sh");
-    prepared.arg("-lc").arg(command).current_dir(cwd);
-    if sandbox_status.filesystem_active {
-        prepared.env("HOME", cwd.join(".sandbox-home"));
-        prepared.env("TMPDIR", cwd.join(".sandbox-tmp"));
-    }
-    prepared
-}
-
-fn prepare_sandbox_dirs(cwd: &std::path::Path) {
-    let _ = std::fs::create_dir_all(cwd.join(".sandbox-home"));
-    let _ = std::fs::create_dir_all(cwd.join(".sandbox-tmp"));
-}
-
 #[cfg(test)]
 mod tests {
     use super::{execute_bash, BashCommandInput};
-    use crate::sandbox::FilesystemIsolationMode;
 
     #[test]
     fn executes_simple_command() {
@@ -251,33 +151,10 @@ mod tests {
             description: None,
             run_in_background: Some(false),
             dangerously_disable_sandbox: Some(false),
-            namespace_restrictions: Some(false),
-            isolate_network: Some(false),
-            filesystem_mode: Some(FilesystemIsolationMode::WorkspaceOnly),
-            allowed_mounts: None,
         })
         .expect("bash command should execute");
 
         assert_eq!(output.stdout, "hello");
         assert!(!output.interrupted);
-        assert!(output.sandbox_status.is_some());
-    }
-
-    #[test]
-    fn disables_sandbox_when_requested() {
-        let output = execute_bash(BashCommandInput {
-            command: String::from("printf 'hello'"),
-            timeout: Some(1_000),
-            description: None,
-            run_in_background: Some(false),
-            dangerously_disable_sandbox: Some(true),
-            namespace_restrictions: None,
-            isolate_network: None,
-            filesystem_mode: None,
-            allowed_mounts: None,
-        })
-        .expect("bash command should execute");
-
-        assert!(!output.sandbox_status.expect("sandbox status").enabled);
     }
 }

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/config.rs

@@ -4,7 +4,6 @@ use std::fs;
 use std::path::{Path, PathBuf};
 
 use crate::json::JsonValue;
-use crate::sandbox::{FilesystemIsolationMode, SandboxConfig};
 
 pub const CLAUDE_CODE_SETTINGS_SCHEMA_NAME: &str = "SettingsSchema";
 
@@ -41,7 +40,6 @@ pub struct RuntimeFeatureConfig {
     oauth: Option<OAuthConfig>,
     model: Option<String>,
     permission_mode: Option<ResolvedPermissionMode>,
-    sandbox: SandboxConfig,
 }
 
 #[derive(Debug, Clone, PartialEq, Eq, Default)]
@@ -227,7 +225,6 @@ impl ConfigLoader {
             oauth: parse_optional_oauth_config(&merged_value, "merged settings.oauth")?,
             model: parse_optional_model(&merged_value),
             permission_mode: parse_optional_permission_mode(&merged_value)?,
-            sandbox: parse_optional_sandbox_config(&merged_value)?,
         };
 
         Ok(RuntimeConfig {
@@ -292,11 +289,6 @@ impl RuntimeConfig {
     pub fn permission_mode(&self) -> Option<ResolvedPermissionMode> {
         self.feature_config.permission_mode
     }
-
-    #[must_use]
-    pub fn sandbox(&self) -> &SandboxConfig {
-        &self.feature_config.sandbox
-    }
 }
 
 impl RuntimeFeatureConfig {
@@ -319,11 +311,6 @@ impl RuntimeFeatureConfig {
     pub fn permission_mode(&self) -> Option<ResolvedPermissionMode> {
         self.permission_mode
     }
-
-    #[must_use]
-    pub fn sandbox(&self) -> &SandboxConfig {
-        &self.sandbox
-    }
 }
 
 impl McpConfigCollection {
@@ -458,42 +445,6 @@ fn parse_permission_mode_label(
     }
 }
 
-fn parse_optional_sandbox_config(root: &JsonValue) -> Result<SandboxConfig, ConfigError> {
-    let Some(object) = root.as_object() else {
-        return Ok(SandboxConfig::default());
-    };
-    let Some(sandbox_value) = object.get("sandbox") else {
-        return Ok(SandboxConfig::default());
-    };
-    let sandbox = expect_object(sandbox_value, "merged settings.sandbox")?;
-    let filesystem_mode = optional_string(sandbox, "filesystemMode", "merged settings.sandbox")?
-        .map(parse_filesystem_mode_label)
-        .transpose()?;
-    Ok(SandboxConfig {
-        enabled: optional_bool(sandbox, "enabled", "merged settings.sandbox")?,
-        namespace_restrictions: optional_bool(
-            sandbox,
-            "namespaceRestrictions",
-            "merged settings.sandbox",
-        )?,
-        network_isolation: optional_bool(sandbox, "networkIsolation", "merged settings.sandbox")?,
-        filesystem_mode,
-        allowed_mounts: optional_string_array(sandbox, "allowedMounts", "merged settings.sandbox")?
-            .unwrap_or_default(),
-    })
-}
-
-fn parse_filesystem_mode_label(value: &str) -> Result<FilesystemIsolationMode, ConfigError> {
-    match value {
-        "off" => Ok(FilesystemIsolationMode::Off),
-        "workspace-only" => Ok(FilesystemIsolationMode::WorkspaceOnly),
-        "allow-list" => Ok(FilesystemIsolationMode::AllowList),
-        other => Err(ConfigError::Parse(format!(
-            "merged settings.sandbox.filesystemMode: unsupported filesystem mode {other}"
-        ))),
-    }
-}
-
 fn parse_optional_oauth_config(
     root: &JsonValue,
     context: &str,
@@ -737,7 +688,6 @@ mod tests {
         CLAUDE_CODE_SETTINGS_SCHEMA_NAME,
     };
     use crate::json::JsonValue;
-    use crate::sandbox::FilesystemIsolationMode;
     use std::fs;
     use std::time::{SystemTime, UNIX_EPOCH};
 
@@ -842,44 +792,6 @@ mod tests {
         fs::remove_dir_all(root).expect("cleanup temp dir");
     }
 
-    #[test]
-    fn parses_sandbox_config() {
-        let root = temp_dir();
-        let cwd = root.join("project");
-        let home = root.join("home").join(".claude");
-        fs::create_dir_all(cwd.join(".claude")).expect("project config dir");
-        fs::create_dir_all(&home).expect("home config dir");
-
-        fs::write(
-            cwd.join(".claude").join("settings.local.json"),
-            r#"{
-              "sandbox": {
-                "enabled": true,
-                "namespaceRestrictions": false,
-                "networkIsolation": true,
-                "filesystemMode": "allow-list",
-                "allowedMounts": ["logs", "tmp/cache"]
-              }
-            }"#,
-        )
-        .expect("write local settings");
-
-        let loaded = ConfigLoader::new(&cwd, &home)
-            .load()
-            .expect("config should load");
-
-        assert_eq!(loaded.sandbox().enabled, Some(true));
-        assert_eq!(loaded.sandbox().namespace_restrictions, Some(false));
-        assert_eq!(loaded.sandbox().network_isolation, Some(true));
-        assert_eq!(
-            loaded.sandbox().filesystem_mode,
-            Some(FilesystemIsolationMode::AllowList)
-        );
-        assert_eq!(loaded.sandbox().allowed_mounts, vec!["logs", "tmp/cache"]);
-
-        fs::remove_dir_all(root).expect("cleanup temp dir");
-    }
-
     #[test]
     fn parses_typed_mcp_and_oauth_config() {
         let root = temp_dir();

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/lib.rs

@@ -12,7 +12,6 @@ mod oauth;
 mod permissions;
 mod prompt;
 mod remote;
-mod sandbox;
 mod session;
 mod usage;
 
@@ -74,12 +73,6 @@ pub use remote::{
     RemoteSessionContext, UpstreamProxyBootstrap, UpstreamProxyState, DEFAULT_REMOTE_BASE_URL,
     DEFAULT_SESSION_TOKEN_PATH, DEFAULT_SYSTEM_CA_BUNDLE, NO_PROXY_HOSTS, UPSTREAM_PROXY_ENV_KEYS,
 };
-pub use sandbox::{
-    build_linux_sandbox_command, detect_container_environment, detect_container_environment_from,
-    resolve_sandbox_status, resolve_sandbox_status_for_request, ContainerEnvironment,
-    FilesystemIsolationMode, LinuxSandboxCommand, SandboxConfig, SandboxDetectionInputs,
-    SandboxRequest, SandboxStatus,
-};
 pub use session::{ContentBlock, ConversationMessage, MessageRole, Session, SessionError};
 pub use usage::{
     format_usd, pricing_for_model, ModelPricing, TokenUsage, UsageCostEstimate, UsageTracker,

rust/crates/runtime/src/permissions.rs

@@ -5,8 +5,6 @@ pub enum PermissionMode {
     ReadOnly,
     WorkspaceWrite,
     DangerFullAccess,
-    Prompt,
-    Allow,
 }
 
 impl PermissionMode {
@@ -16,8 +14,6 @@ impl PermissionMode {
             Self::ReadOnly => "read-only",
             Self::WorkspaceWrite => "workspace-write",
             Self::DangerFullAccess => "danger-full-access",
-            Self::Prompt => "prompt",
-            Self::Allow => "allow",
         }
     }
 }
@@ -94,7 +90,7 @@ impl PermissionPolicy {
     ) -> PermissionOutcome {
         let current_mode = self.active_mode();
         let required_mode = self.required_mode_for(tool_name);
-        if current_mode == PermissionMode::Allow || current_mode >= required_mode {
+        if current_mode >= required_mode {
             return PermissionOutcome::Allow;
         }
 
@@ -105,9 +101,8 @@ impl PermissionPolicy {
             required_mode,
         };
 
-        if current_mode == PermissionMode::Prompt
-            || (current_mode == PermissionMode::WorkspaceWrite
-                && required_mode == PermissionMode::DangerFullAccess)
+        if current_mode == PermissionMode::WorkspaceWrite
+            && required_mode == PermissionMode::DangerFullAccess
         {
             return match prompter.as_mut() {
                 Some(prompter) => match prompter.decide(&request) {

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,
-        ContextFile, ProjectContext, SystemPromptBuilder, SYSTEM_PROMPT_DYNAMIC_BOUNDARY,
+        render_instruction_content, render_instruction_files, render_memory_files,
+        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/runtime/src/sandbox.rs

@@ -1,364 +0,0 @@
-use std::env;
-use std::fs;
-use std::path::{Path, PathBuf};
-
-use serde::{Deserialize, Serialize};
-
-#[derive(Debug, Clone, Copy, Serialize, Deserialize, PartialEq, Eq, Default)]
-#[serde(rename_all = "kebab-case")]
-pub enum FilesystemIsolationMode {
-    Off,
-    #[default]
-    WorkspaceOnly,
-    AllowList,
-}
-
-impl FilesystemIsolationMode {
-    #[must_use]
-    pub fn as_str(self) -> &'static str {
-        match self {
-            Self::Off => "off",
-            Self::WorkspaceOnly => "workspace-only",
-            Self::AllowList => "allow-list",
-        }
-    }
-}
-
-#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Eq, Default)]
-pub struct SandboxConfig {
-    pub enabled: Option<bool>,
-    pub namespace_restrictions: Option<bool>,
-    pub network_isolation: Option<bool>,
-    pub filesystem_mode: Option<FilesystemIsolationMode>,
-    pub allowed_mounts: Vec<String>,
-}
-
-#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Eq, Default)]
-pub struct SandboxRequest {
-    pub enabled: bool,
-    pub namespace_restrictions: bool,
-    pub network_isolation: bool,
-    pub filesystem_mode: FilesystemIsolationMode,
-    pub allowed_mounts: Vec<String>,
-}
-
-#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Eq, Default)]
-pub struct ContainerEnvironment {
-    pub in_container: bool,
-    pub markers: Vec<String>,
-}
-
-#[allow(clippy::struct_excessive_bools)]
-#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Eq, Default)]
-pub struct SandboxStatus {
-    pub enabled: bool,
-    pub requested: SandboxRequest,
-    pub supported: bool,
-    pub active: bool,
-    pub namespace_supported: bool,
-    pub namespace_active: bool,
-    pub network_supported: bool,
-    pub network_active: bool,
-    pub filesystem_mode: FilesystemIsolationMode,
-    pub filesystem_active: bool,
-    pub allowed_mounts: Vec<String>,
-    pub in_container: bool,
-    pub container_markers: Vec<String>,
-    pub fallback_reason: Option<String>,
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-pub struct SandboxDetectionInputs<'a> {
-    pub env_pairs: Vec<(String, String)>,
-    pub dockerenv_exists: bool,
-    pub containerenv_exists: bool,
-    pub proc_1_cgroup: Option<&'a str>,
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-pub struct LinuxSandboxCommand {
-    pub program: String,
-    pub args: Vec<String>,
-    pub env: Vec<(String, String)>,
-}
-
-impl SandboxConfig {
-    #[must_use]
-    pub fn resolve_request(
-        &self,
-        enabled_override: Option<bool>,
-        namespace_override: Option<bool>,
-        network_override: Option<bool>,
-        filesystem_mode_override: Option<FilesystemIsolationMode>,
-        allowed_mounts_override: Option<Vec<String>>,
-    ) -> SandboxRequest {
-        SandboxRequest {
-            enabled: enabled_override.unwrap_or(self.enabled.unwrap_or(true)),
-            namespace_restrictions: namespace_override
-                .unwrap_or(self.namespace_restrictions.unwrap_or(true)),
-            network_isolation: network_override.unwrap_or(self.network_isolation.unwrap_or(false)),
-            filesystem_mode: filesystem_mode_override
-                .or(self.filesystem_mode)
-                .unwrap_or_default(),
-            allowed_mounts: allowed_mounts_override.unwrap_or_else(|| self.allowed_mounts.clone()),
-        }
-    }
-}
-
-#[must_use]
-pub fn detect_container_environment() -> ContainerEnvironment {
-    let proc_1_cgroup = fs::read_to_string("/proc/1/cgroup").ok();
-    detect_container_environment_from(SandboxDetectionInputs {
-        env_pairs: env::vars().collect(),
-        dockerenv_exists: Path::new("/.dockerenv").exists(),
-        containerenv_exists: Path::new("/run/.containerenv").exists(),
-        proc_1_cgroup: proc_1_cgroup.as_deref(),
-    })
-}
-
-#[must_use]
-pub fn detect_container_environment_from(
-    inputs: SandboxDetectionInputs<'_>,
-) -> ContainerEnvironment {
-    let mut markers = Vec::new();
-    if inputs.dockerenv_exists {
-        markers.push("/.dockerenv".to_string());
-    }
-    if inputs.containerenv_exists {
-        markers.push("/run/.containerenv".to_string());
-    }
-    for (key, value) in inputs.env_pairs {
-        let normalized = key.to_ascii_lowercase();
-        if matches!(
-            normalized.as_str(),
-            "container" | "docker" | "podman" | "kubernetes_service_host"
-        ) && !value.is_empty()
-        {
-            markers.push(format!("env:{key}={value}"));
-        }
-    }
-    if let Some(cgroup) = inputs.proc_1_cgroup {
-        for needle in ["docker", "containerd", "kubepods", "podman", "libpod"] {
-            if cgroup.contains(needle) {
-                markers.push(format!("/proc/1/cgroup:{needle}"));
-            }
-        }
-    }
-    markers.sort();
-    markers.dedup();
-    ContainerEnvironment {
-        in_container: !markers.is_empty(),
-        markers,
-    }
-}
-
-#[must_use]
-pub fn resolve_sandbox_status(config: &SandboxConfig, cwd: &Path) -> SandboxStatus {
-    let request = config.resolve_request(None, None, None, None, None);
-    resolve_sandbox_status_for_request(&request, cwd)
-}
-
-#[must_use]
-pub fn resolve_sandbox_status_for_request(request: &SandboxRequest, cwd: &Path) -> SandboxStatus {
-    let container = detect_container_environment();
-    let namespace_supported = cfg!(target_os = "linux") && command_exists("unshare");
-    let network_supported = namespace_supported;
-    let filesystem_active =
-        request.enabled && request.filesystem_mode != FilesystemIsolationMode::Off;
-    let mut fallback_reasons = Vec::new();
-
-    if request.enabled && request.namespace_restrictions && !namespace_supported {
-        fallback_reasons
-            .push("namespace isolation unavailable (requires Linux with `unshare`)".to_string());
-    }
-    if request.enabled && request.network_isolation && !network_supported {
-        fallback_reasons
-            .push("network isolation unavailable (requires Linux with `unshare`)".to_string());
-    }
-    if request.enabled
-        && request.filesystem_mode == FilesystemIsolationMode::AllowList
-        && request.allowed_mounts.is_empty()
-    {
-        fallback_reasons
-            .push("filesystem allow-list requested without configured mounts".to_string());
-    }
-
-    let active = request.enabled
-        && (!request.namespace_restrictions || namespace_supported)
-        && (!request.network_isolation || network_supported);
-
-    let allowed_mounts = normalize_mounts(&request.allowed_mounts, cwd);
-
-    SandboxStatus {
-        enabled: request.enabled,
-        requested: request.clone(),
-        supported: namespace_supported,
-        active,
-        namespace_supported,
-        namespace_active: request.enabled && request.namespace_restrictions && namespace_supported,
-        network_supported,
-        network_active: request.enabled && request.network_isolation && network_supported,
-        filesystem_mode: request.filesystem_mode,
-        filesystem_active,
-        allowed_mounts,
-        in_container: container.in_container,
-        container_markers: container.markers,
-        fallback_reason: (!fallback_reasons.is_empty()).then(|| fallback_reasons.join("; ")),
-    }
-}
-
-#[must_use]
-pub fn build_linux_sandbox_command(
-    command: &str,
-    cwd: &Path,
-    status: &SandboxStatus,
-) -> Option<LinuxSandboxCommand> {
-    if !cfg!(target_os = "linux")
-        || !status.enabled
-        || (!status.namespace_active && !status.network_active)
-    {
-        return None;
-    }
-
-    let mut args = vec![
-        "--user".to_string(),
-        "--map-root-user".to_string(),
-        "--mount".to_string(),
-        "--ipc".to_string(),
-        "--pid".to_string(),
-        "--uts".to_string(),
-        "--fork".to_string(),
-    ];
-    if status.network_active {
-        args.push("--net".to_string());
-    }
-    args.push("sh".to_string());
-    args.push("-lc".to_string());
-    args.push(command.to_string());
-
-    let sandbox_home = cwd.join(".sandbox-home");
-    let sandbox_tmp = cwd.join(".sandbox-tmp");
-    let mut env = vec![
-        ("HOME".to_string(), sandbox_home.display().to_string()),
-        ("TMPDIR".to_string(), sandbox_tmp.display().to_string()),
-        (
-            "CLAWD_SANDBOX_FILESYSTEM_MODE".to_string(),
-            status.filesystem_mode.as_str().to_string(),
-        ),
-        (
-            "CLAWD_SANDBOX_ALLOWED_MOUNTS".to_string(),
-            status.allowed_mounts.join(":"),
-        ),
-    ];
-    if let Ok(path) = env::var("PATH") {
-        env.push(("PATH".to_string(), path));
-    }
-
-    Some(LinuxSandboxCommand {
-        program: "unshare".to_string(),
-        args,
-        env,
-    })
-}
-
-fn normalize_mounts(mounts: &[String], cwd: &Path) -> Vec<String> {
-    let cwd = cwd.to_path_buf();
-    mounts
-        .iter()
-        .map(|mount| {
-            let path = PathBuf::from(mount);
-            if path.is_absolute() {
-                path
-            } else {
-                cwd.join(path)
-            }
-        })
-        .map(|path| path.display().to_string())
-        .collect()
-}
-
-fn command_exists(command: &str) -> bool {
-    env::var_os("PATH")
-        .is_some_and(|paths| env::split_paths(&paths).any(|path| path.join(command).exists()))
-}
-
-#[cfg(test)]
-mod tests {
-    use super::{
-        build_linux_sandbox_command, detect_container_environment_from, FilesystemIsolationMode,
-        SandboxConfig, SandboxDetectionInputs,
-    };
-    use std::path::Path;
-
-    #[test]
-    fn detects_container_markers_from_multiple_sources() {
-        let detected = detect_container_environment_from(SandboxDetectionInputs {
-            env_pairs: vec![("container".to_string(), "docker".to_string())],
-            dockerenv_exists: true,
-            containerenv_exists: false,
-            proc_1_cgroup: Some("12:memory:/docker/abc"),
-        });
-
-        assert!(detected.in_container);
-        assert!(detected
-            .markers
-            .iter()
-            .any(|marker| marker == "/.dockerenv"));
-        assert!(detected
-            .markers
-            .iter()
-            .any(|marker| marker == "env:container=docker"));
-        assert!(detected
-            .markers
-            .iter()
-            .any(|marker| marker == "/proc/1/cgroup:docker"));
-    }
-
-    #[test]
-    fn resolves_request_with_overrides() {
-        let config = SandboxConfig {
-            enabled: Some(true),
-            namespace_restrictions: Some(true),
-            network_isolation: Some(false),
-            filesystem_mode: Some(FilesystemIsolationMode::WorkspaceOnly),
-            allowed_mounts: vec!["logs".to_string()],
-        };
-
-        let request = config.resolve_request(
-            Some(true),
-            Some(false),
-            Some(true),
-            Some(FilesystemIsolationMode::AllowList),
-            Some(vec!["tmp".to_string()]),
-        );
-
-        assert!(request.enabled);
-        assert!(!request.namespace_restrictions);
-        assert!(request.network_isolation);
-        assert_eq!(request.filesystem_mode, FilesystemIsolationMode::AllowList);
-        assert_eq!(request.allowed_mounts, vec!["tmp"]);
-    }
-
-    #[test]
-    fn builds_linux_launcher_with_network_flag_when_requested() {
-        let config = SandboxConfig::default();
-        let status = super::resolve_sandbox_status_for_request(
-            &config.resolve_request(
-                Some(true),
-                Some(true),
-                Some(true),
-                Some(FilesystemIsolationMode::WorkspaceOnly),
-                None,
-            ),
-            Path::new("/workspace"),
-        );
-
-        if let Some(launcher) =
-            build_linux_sandbox_command("printf hi", Path::new("/workspace"), &status)
-        {
-            assert_eq!(launcher.program, "unshare");
-            assert!(launcher.args.iter().any(|arg| arg == "--mount"));
-            assert!(launcher.args.iter().any(|arg| arg == "--net") == status.network_active);
-        }
-    }
-}

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

@@ -23,8 +23,8 @@ use compat_harness::{extract_manifest, UpstreamPaths};
 use render::{Spinner, TerminalRenderer};
 use runtime::{
     clear_oauth_credentials, generate_pkce_pair, generate_state, load_system_prompt,
-    parse_oauth_callback_request_target, resolve_sandbox_status, save_oauth_credentials, ApiClient,
-    ApiRequest, AssistantEvent, CompactionConfig, ConfigLoader, ConfigSource, ContentBlock,
+    parse_oauth_callback_request_target, save_oauth_credentials, ApiClient, ApiRequest,
+    AssistantEvent, CompactionConfig, ConfigLoader, ConfigSource, ContentBlock,
     ConversationMessage, ConversationRuntime, MessageRole, OAuthAuthorizationRequest,
     OAuthTokenExchangeRequest, PermissionMode, PermissionPolicy, ProjectContext, RuntimeError,
     Session, TokenUsage, ToolError, ToolExecutor, UsageTracker,
@@ -591,7 +591,6 @@ struct StatusContext {
     memory_file_count: usize,
     project_root: Option<PathBuf>,
     git_branch: Option<String>,
-    sandbox_status: runtime::SandboxStatus,
 }
 
 #[derive(Debug, Clone, Copy)]
@@ -841,18 +840,6 @@ fn run_resume_command(
                 )),
             })
         }
-        SlashCommand::Sandbox => {
-            let cwd = env::current_dir()?;
-            let loader = ConfigLoader::default_for(&cwd);
-            let runtime_config = loader.load()?;
-            Ok(ResumeCommandOutcome {
-                session: session.clone(),
-                message: Some(format_sandbox_report(&resolve_sandbox_status(
-                    runtime_config.sandbox(),
-                    &cwd,
-                ))),
-            })
-        }
         SlashCommand::Cost => {
             let usage = UsageTracker::from_session(session).cumulative_usage();
             Ok(ResumeCommandOutcome {
@@ -1104,10 +1091,6 @@ impl LiveCli {
                 self.print_status();
                 false
             }
-            SlashCommand::Sandbox => {
-                Self::print_sandbox_status();
-                false
-            }
             SlashCommand::Compact => {
                 self.compact()?;
                 false
@@ -1179,18 +1162,6 @@ impl LiveCli {
         );
     }
 
-    fn print_sandbox_status() {
-        let cwd = env::current_dir().expect("current dir");
-        let loader = ConfigLoader::default_for(&cwd);
-        let runtime_config = loader
-            .load()
-            .unwrap_or_else(|_| runtime::RuntimeConfig::empty());
-        println!(
-            "{}",
-            format_sandbox_report(&resolve_sandbox_status(runtime_config.sandbox(), &cwd))
-        );
-    }
-
     fn set_model(&mut self, model: Option<String>) -> Result<bool, Box<dyn std::error::Error>> {
         let Some(model) = model else {
             println!(
@@ -1566,16 +1537,15 @@ fn status_context(
     let project_context = ProjectContext::discover_with_git(&cwd, DEFAULT_DATE)?;
     let (project_root, git_branch) =
         parse_git_status_metadata(project_context.git_status.as_deref());
-    let sandbox_status = resolve_sandbox_status(runtime_config.sandbox(), &cwd);
     Ok(StatusContext {
         cwd,
         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,
-        sandbox_status,
     })
 }
 
@@ -1628,7 +1598,6 @@ fn format_status_report(
             context.discovered_config_files,
             context.memory_file_count,
         ),
-        format_sandbox_report(&context.sandbox_status),
     ]
     .join(
         "
@@ -1637,49 +1606,6 @@ fn format_status_report(
     )
 }
 
-fn format_sandbox_report(status: &runtime::SandboxStatus) -> String {
-    format!(
-        "Sandbox
-  Enabled           {}
-  Active            {}
-  Supported         {}
-  In container      {}
-  Requested ns      {}
-  Active ns         {}
-  Requested net     {}
-  Active net        {}
-  Filesystem mode   {}
-  Filesystem active {}
-  Allowed mounts    {}
-  Markers           {}
-  Fallback reason   {}",
-        status.enabled,
-        status.active,
-        status.supported,
-        status.in_container,
-        status.requested.namespace_restrictions,
-        status.namespace_active,
-        status.requested.network_isolation,
-        status.network_active,
-        status.filesystem_mode.as_str(),
-        status.filesystem_active,
-        if status.allowed_mounts.is_empty() {
-            "<none>".to_string()
-        } else {
-            status.allowed_mounts.join(", ")
-        },
-        if status.container_markers.is_empty() {
-            "<none>".to_string()
-        } else {
-            status.container_markers.join(", ")
-        },
-        status
-            .fallback_reason
-            .clone()
-            .unwrap_or_else(|| "<none>".to_string()),
-    )
-}
-
 fn render_config_report(section: Option<&str>) -> Result<String, Box<dyn std::error::Error>> {
     let cwd = env::current_dir()?;
     let loader = ConfigLoader::default_for(&cwd);
@@ -1762,39 +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() {
-        lines.push("Discovered files".to_string());
-        lines.push(
-            "  No CLAUDE instruction files discovered in the current directory ancestry."
-                .to_string(),
-        );
-    } else {
-        lines.push("Discovered files".to_string());
-        for (index, file) in project_context.instruction_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
-            ));
-        }
-    }
+    append_memory_section(
+        &mut lines,
+        "Instruction files",
+        &project_context.instruction_files,
+        "No CLAUDE instruction files discovered in the current directory ancestry.",
+    );
+    append_memory_section(
+        &mut lines,
+        "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!(
+            "     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");
@@ -2676,7 +2621,6 @@ mod tests {
         assert!(help.contains("REPL"));
         assert!(help.contains("/help"));
         assert!(help.contains("/status"));
-        assert!(help.contains("/sandbox"));
         assert!(help.contains("/model [model]"));
         assert!(help.contains("/permissions [read-only|workspace-write|danger-full-access]"));
         assert!(help.contains("/clear [--confirm]"));
@@ -2701,8 +2645,8 @@ mod tests {
         assert_eq!(
             names,
             vec![
-                "help", "status", "sandbox", "compact", "clear", "cost", "config", "memory",
-                "init", "diff", "version", "export",
+                "help", "status", "compact", "clear", "cost", "config", "memory", "init", "diff",
+                "version", "export",
             ]
         );
     }
@@ -2820,7 +2764,6 @@ mod tests {
                 memory_file_count: 4,
                 project_root: Some(PathBuf::from("/tmp")),
                 git_branch: Some("main".to_string()),
-                sandbox_status: runtime::SandboxStatus::default(),
             },
         );
         assert!(status.contains("Status"));
@@ -2849,7 +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]
@@ -2874,7 +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);
     }
 
@@ -2982,17 +2925,3 @@ mod tests {
         assert!(done.contains("contents"));
     }
 }
-
-#[cfg(test)]
-mod sandbox_report_tests {
-    use super::format_sandbox_report;
-
-    #[test]
-    fn sandbox_report_renders_expected_fields() {
-        let report = format_sandbox_report(&runtime::SandboxStatus::default());
-        assert!(report.contains("Sandbox"));
-        assert!(report.contains("Enabled"));
-        assert!(report.contains("Filesystem mode"));
-        assert!(report.contains("Fallback reason"));
-    }
-}

rust/crates/tools/src/lib.rs

@@ -62,11 +62,7 @@ pub fn mvp_tool_specs() -> Vec<ToolSpec> {
                     "timeout": { "type": "integer", "minimum": 1 },
                     "description": { "type": "string" },
                     "run_in_background": { "type": "boolean" },
-                    "dangerouslyDisableSandbox": { "type": "boolean" },
-                    "namespaceRestrictions": { "type": "boolean" },
-                    "isolateNetwork": { "type": "boolean" },
-                    "filesystemMode": { "type": "string", "enum": ["off", "workspace-only", "allow-list"] },
-                    "allowedMounts": { "type": "array", "items": { "type": "string" } }
+                    "dangerouslyDisableSandbox": { "type": "boolean" }
                 },
                 "required": ["command"],
                 "additionalProperties": false
@@ -1203,10 +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()
     };
@@ -1224,11 +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(
-        &store_path,
-        serde_json::to_string_pretty(&persisted).map_err(|error| error.to_string())?,
-    )
-    .map_err(|error| error.to_string())?;
+    std::fs::write(&store_path, render_todo_markdown(&persisted))
+        .map_err(|error| error.to_string())?;
 
     let verification_nudge_needed = (all_done
         && input.todos.len() >= 3
@@ -1286,7 +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> {
@@ -2218,7 +2261,6 @@ fn execute_shell_command(
             structured_content: None,
             persisted_output_path: None,
             persisted_output_size: None,
-            sandbox_status: None,
         });
     }
 
@@ -2256,7 +2298,6 @@ fn execute_shell_command(
                     structured_content: None,
                     persisted_output_path: None,
                     persisted_output_size: None,
-                    sandbox_status: None,
                 });
             }
             if started.elapsed() >= Duration::from_millis(timeout_ms) {
@@ -2287,7 +2328,6 @@ Command exceeded timeout of {timeout_ms} ms",
                     structured_content: None,
                     persisted_output_path: None,
                     persisted_output_size: None,
-                    sandbox_status: None,
                 });
             }
             std::thread::sleep(Duration::from_millis(10));
@@ -2314,7 +2354,6 @@ Command exceeded timeout of {timeout_ms} ms",
         structured_content: None,
         persisted_output_path: None,
         persisted_output_size: None,
-        sandbox_status: None,
     })
 }
 
@@ -2646,6 +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()