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/.omc/project-memory.json

@@ -1,127 +0,0 @@
-{
-  "version": "1.0.0",
-  "lastScanned": 1774971516826,
-  "projectRoot": "/home/bellman/Workspace/clawd-code-worktrees/api/rust",
-  "techStack": {
-    "languages": [
-      {
-        "name": "Rust",
-        "version": null,
-        "confidence": "high",
-        "markers": [
-          "Cargo.toml"
-        ]
-      }
-    ],
-    "frameworks": [],
-    "packageManager": "cargo",
-    "runtime": null
-  },
-  "build": {
-    "buildCommand": "cargo build",
-    "testCommand": "cargo test",
-    "lintCommand": "cargo clippy",
-    "devCommand": "cargo run",
-    "scripts": {}
-  },
-  "conventions": {
-    "namingStyle": null,
-    "importStyle": null,
-    "testPattern": null,
-    "fileOrganization": null
-  },
-  "structure": {
-    "isMonorepo": false,
-    "workspaces": [],
-    "mainDirectories": [],
-    "gitBranches": {
-      "defaultBranch": "main",
-      "branchingStrategy": null
-    }
-  },
-  "customNotes": [],
-  "directoryMap": {
-    "crates": {
-      "path": "crates",
-      "purpose": null,
-      "fileCount": 0,
-      "lastAccessed": 1774971516823,
-      "keyFiles": []
-    },
-    "target": {
-      "path": "target",
-      "purpose": null,
-      "fileCount": 2,
-      "lastAccessed": 1774971516823,
-      "keyFiles": [
-        "CACHEDIR.TAG"
-      ]
-    },
-    "crates/api": {
-      "path": "crates/api",
-      "purpose": "API routes",
-      "fileCount": 1,
-      "lastAccessed": 1774971516824,
-      "keyFiles": [
-        "Cargo.toml"
-      ]
-    }
-  },
-  "hotPaths": [
-    {
-      "path": "crates/api/Cargo.toml",
-      "accessCount": 1,
-      "lastAccessed": 1774971547109,
-      "type": "file"
-    },
-    {
-      "path": "crates/api/src/lib.rs",
-      "accessCount": 1,
-      "lastAccessed": 1774971547624,
-      "type": "file"
-    },
-    {
-      "path": "crates/api/src/client.rs",
-      "accessCount": 1,
-      "lastAccessed": 1774971548001,
-      "type": "file"
-    },
-    {
-      "path": "crates/api/src/error.rs",
-      "accessCount": 1,
-      "lastAccessed": 1774971548503,
-      "type": "file"
-    },
-    {
-      "path": "crates/api/src/sse.rs",
-      "accessCount": 1,
-      "lastAccessed": 1774971549311,
-      "type": "file"
-    },
-    {
-      "path": "crates/api/src/types.rs",
-      "accessCount": 1,
-      "lastAccessed": 1774971549472,
-      "type": "file"
-    },
-    {
-      "path": "crates/api/tests/client_integration.rs",
-      "accessCount": 1,
-      "lastAccessed": 1774971550143,
-      "type": "file"
-    },
-    {
-      "path": "Cargo.toml",
-      "accessCount": 1,
-      "lastAccessed": 1774971550539,
-      "type": "file"
-    },
-    {
-      "path": "crates/rusty-claude-cli/src/main.rs",
-      "accessCount": 1,
-      "lastAccessed": 1774971551474,
-      "type": "file"
-    }
-  ],
-  "userDirectives": []
-}

rust/.omc/state/idle-notif-cooldown.json

@@ -1,3 +0,0 @@
-{
-  "lastSentAt": "2026-03-31T15:39:44.771Z"
-}

rust/README.md

@@ -109,13 +109,6 @@ cd rust
 cargo run -p rusty-claude-cli -- --allowedTools read,glob
 ```
 
-Bootstrap Claude project files for the current repo:
-
-```bash
-cd rust
-cargo run -p rusty-claude-cli -- init
-```
-
 ### 2) REPL mode
 
 Start the interactive shell:
@@ -186,7 +179,7 @@ cargo run -p rusty-claude-cli -- --resume session.json /memory /config
 - `/resume <session-path>` — load a saved session into the REPL
 - `/config [env|hooks|model]` — inspect discovered Claude config
 - `/memory` — inspect loaded instruction memory files
-- `/init` — bootstrap `.claude.json`, `.claude/`, `CLAUDE.md`, and local ignore rules
+- `/init` — create a starter `CLAUDE.md`
 - `/diff` — show the current git diff for the workspace
 - `/version` — print version and build metadata locally
 - `/export [file]` — export the current conversation transcript

rust/crates/commands/src/lib.rs

@@ -101,7 +101,7 @@ const SLASH_COMMAND_SPECS: &[SlashCommandSpec] = &[
     },
     SlashCommandSpec {
         name: "init",
-        summary: "Bootstrap Claude project files for this repo",
+        summary: "Create a starter CLAUDE.md for this repo",
         argument_hint: None,
         resume_supported: true,
     },

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,
-        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/rusty-claude-cli/src/init.rs

@@ -1,433 +0,0 @@
-use std::fs;
-use std::path::{Path, PathBuf};
-
-const STARTER_CLAUDE_JSON: &str = concat!(
-    "{\n",
-    "  \"permissions\": {\n",
-    "    \"defaultMode\": \"acceptEdits\"\n",
-    "  }\n",
-    "}\n",
-);
-const GITIGNORE_COMMENT: &str = "# Claude Code local artifacts";
-const GITIGNORE_ENTRIES: [&str; 2] = [".claude/settings.local.json", ".claude/sessions/"];
-
-#[derive(Debug, Clone, Copy, PartialEq, Eq)]
-pub(crate) enum InitStatus {
-    Created,
-    Updated,
-    Skipped,
-}
-
-impl InitStatus {
-    #[must_use]
-    pub(crate) fn label(self) -> &'static str {
-        match self {
-            Self::Created => "created",
-            Self::Updated => "updated",
-            Self::Skipped => "skipped (already exists)",
-        }
-    }
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-pub(crate) struct InitArtifact {
-    pub(crate) name: &'static str,
-    pub(crate) status: InitStatus,
-}
-
-#[derive(Debug, Clone, PartialEq, Eq)]
-pub(crate) struct InitReport {
-    pub(crate) project_root: PathBuf,
-    pub(crate) artifacts: Vec<InitArtifact>,
-}
-
-impl InitReport {
-    #[must_use]
-    pub(crate) fn render(&self) -> String {
-        let mut lines = vec![
-            "Init".to_string(),
-            format!("  Project          {}", self.project_root.display()),
-        ];
-        for artifact in &self.artifacts {
-            lines.push(format!(
-                "  {:<16} {}",
-                artifact.name,
-                artifact.status.label()
-            ));
-        }
-        lines.push("  Next step        Review and tailor the generated guidance".to_string());
-        lines.join("\n")
-    }
-}
-
-#[derive(Debug, Clone, Default, PartialEq, Eq)]
-#[allow(clippy::struct_excessive_bools)]
-struct RepoDetection {
-    rust_workspace: bool,
-    rust_root: bool,
-    python: bool,
-    package_json: bool,
-    typescript: bool,
-    nextjs: bool,
-    react: bool,
-    vite: bool,
-    nest: bool,
-    src_dir: bool,
-    tests_dir: bool,
-    rust_dir: bool,
-}
-
-pub(crate) fn initialize_repo(cwd: &Path) -> Result<InitReport, Box<dyn std::error::Error>> {
-    let mut artifacts = Vec::new();
-
-    let claude_dir = cwd.join(".claude");
-    artifacts.push(InitArtifact {
-        name: ".claude/",
-        status: ensure_dir(&claude_dir)?,
-    });
-
-    let claude_json = cwd.join(".claude.json");
-    artifacts.push(InitArtifact {
-        name: ".claude.json",
-        status: write_file_if_missing(&claude_json, STARTER_CLAUDE_JSON)?,
-    });
-
-    let gitignore = cwd.join(".gitignore");
-    artifacts.push(InitArtifact {
-        name: ".gitignore",
-        status: ensure_gitignore_entries(&gitignore)?,
-    });
-
-    let claude_md = cwd.join("CLAUDE.md");
-    let content = render_init_claude_md(cwd);
-    artifacts.push(InitArtifact {
-        name: "CLAUDE.md",
-        status: write_file_if_missing(&claude_md, &content)?,
-    });
-
-    Ok(InitReport {
-        project_root: cwd.to_path_buf(),
-        artifacts,
-    })
-}
-
-fn ensure_dir(path: &Path) -> Result<InitStatus, std::io::Error> {
-    if path.is_dir() {
-        return Ok(InitStatus::Skipped);
-    }
-    fs::create_dir_all(path)?;
-    Ok(InitStatus::Created)
-}
-
-fn write_file_if_missing(path: &Path, content: &str) -> Result<InitStatus, std::io::Error> {
-    if path.exists() {
-        return Ok(InitStatus::Skipped);
-    }
-    fs::write(path, content)?;
-    Ok(InitStatus::Created)
-}
-
-fn ensure_gitignore_entries(path: &Path) -> Result<InitStatus, std::io::Error> {
-    if !path.exists() {
-        let mut lines = vec![GITIGNORE_COMMENT.to_string()];
-        lines.extend(GITIGNORE_ENTRIES.iter().map(|entry| (*entry).to_string()));
-        fs::write(path, format!("{}\n", lines.join("\n")))?;
-        return Ok(InitStatus::Created);
-    }
-
-    let existing = fs::read_to_string(path)?;
-    let mut lines = existing.lines().map(ToOwned::to_owned).collect::<Vec<_>>();
-    let mut changed = false;
-
-    if !lines.iter().any(|line| line == GITIGNORE_COMMENT) {
-        lines.push(GITIGNORE_COMMENT.to_string());
-        changed = true;
-    }
-
-    for entry in GITIGNORE_ENTRIES {
-        if !lines.iter().any(|line| line == entry) {
-            lines.push(entry.to_string());
-            changed = true;
-        }
-    }
-
-    if !changed {
-        return Ok(InitStatus::Skipped);
-    }
-
-    fs::write(path, format!("{}\n", lines.join("\n")))?;
-    Ok(InitStatus::Updated)
-}
-
-pub(crate) fn render_init_claude_md(cwd: &Path) -> String {
-    let detection = detect_repo(cwd);
-    let mut lines = vec![
-        "# CLAUDE.md".to_string(),
-        String::new(),
-        "This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.".to_string(),
-        String::new(),
-    ];
-
-    let detected_languages = detected_languages(&detection);
-    let detected_frameworks = detected_frameworks(&detection);
-    lines.push("## Detected stack".to_string());
-    if detected_languages.is_empty() {
-        lines.push("- No specific language markers were detected yet; document the primary language and verification commands once the project structure settles.".to_string());
-    } else {
-        lines.push(format!("- Languages: {}.", detected_languages.join(", ")));
-    }
-    if detected_frameworks.is_empty() {
-        lines.push("- Frameworks: none detected from the supported starter markers.".to_string());
-    } else {
-        lines.push(format!(
-            "- Frameworks/tooling markers: {}.",
-            detected_frameworks.join(", ")
-        ));
-    }
-    lines.push(String::new());
-
-    let verification_lines = verification_lines(cwd, &detection);
-    if !verification_lines.is_empty() {
-        lines.push("## Verification".to_string());
-        lines.extend(verification_lines);
-        lines.push(String::new());
-    }
-
-    let structure_lines = repository_shape_lines(&detection);
-    if !structure_lines.is_empty() {
-        lines.push("## Repository shape".to_string());
-        lines.extend(structure_lines);
-        lines.push(String::new());
-    }
-
-    let framework_lines = framework_notes(&detection);
-    if !framework_lines.is_empty() {
-        lines.push("## Framework notes".to_string());
-        lines.extend(framework_lines);
-        lines.push(String::new());
-    }
-
-    lines.push("## Working agreement".to_string());
-    lines.push("- Prefer small, reviewable changes and keep generated bootstrap files aligned with actual repo workflows.".to_string());
-    lines.push("- Keep shared defaults in `.claude.json`; reserve `.claude/settings.local.json` for machine-local overrides.".to_string());
-    lines.push("- Do not overwrite existing `CLAUDE.md` content automatically; update it intentionally when repo workflows change.".to_string());
-    lines.push(String::new());
-
-    lines.join("\n")
-}
-
-fn detect_repo(cwd: &Path) -> RepoDetection {
-    let package_json_contents = fs::read_to_string(cwd.join("package.json"))
-        .unwrap_or_default()
-        .to_ascii_lowercase();
-    RepoDetection {
-        rust_workspace: cwd.join("rust").join("Cargo.toml").is_file(),
-        rust_root: cwd.join("Cargo.toml").is_file(),
-        python: cwd.join("pyproject.toml").is_file()
-            || cwd.join("requirements.txt").is_file()
-            || cwd.join("setup.py").is_file(),
-        package_json: cwd.join("package.json").is_file(),
-        typescript: cwd.join("tsconfig.json").is_file()
-            || package_json_contents.contains("typescript"),
-        nextjs: package_json_contents.contains("\"next\""),
-        react: package_json_contents.contains("\"react\""),
-        vite: package_json_contents.contains("\"vite\""),
-        nest: package_json_contents.contains("@nestjs"),
-        src_dir: cwd.join("src").is_dir(),
-        tests_dir: cwd.join("tests").is_dir(),
-        rust_dir: cwd.join("rust").is_dir(),
-    }
-}
-
-fn detected_languages(detection: &RepoDetection) -> Vec<&'static str> {
-    let mut languages = Vec::new();
-    if detection.rust_workspace || detection.rust_root {
-        languages.push("Rust");
-    }
-    if detection.python {
-        languages.push("Python");
-    }
-    if detection.typescript {
-        languages.push("TypeScript");
-    } else if detection.package_json {
-        languages.push("JavaScript/Node.js");
-    }
-    languages
-}
-
-fn detected_frameworks(detection: &RepoDetection) -> Vec<&'static str> {
-    let mut frameworks = Vec::new();
-    if detection.nextjs {
-        frameworks.push("Next.js");
-    }
-    if detection.react {
-        frameworks.push("React");
-    }
-    if detection.vite {
-        frameworks.push("Vite");
-    }
-    if detection.nest {
-        frameworks.push("NestJS");
-    }
-    frameworks
-}
-
-fn verification_lines(cwd: &Path, detection: &RepoDetection) -> Vec<String> {
-    let mut lines = Vec::new();
-    if detection.rust_workspace {
-        lines.push("- Run Rust verification from `rust/`: `cargo fmt`, `cargo clippy --workspace --all-targets -- -D warnings`, `cargo test --workspace`".to_string());
-    } else if detection.rust_root {
-        lines.push("- Run Rust verification from the repo root: `cargo fmt`, `cargo clippy --workspace --all-targets -- -D warnings`, `cargo test --workspace`".to_string());
-    }
-    if detection.python {
-        if cwd.join("pyproject.toml").is_file() {
-            lines.push("- Run the Python project checks declared in `pyproject.toml` (for example: `pytest`, `ruff check`, and `mypy` when configured).".to_string());
-        } else {
-            lines.push(
-                "- Run the repo's Python test/lint commands before shipping changes.".to_string(),
-            );
-        }
-    }
-    if detection.package_json {
-        lines.push("- Run the JavaScript/TypeScript checks from `package.json` before shipping changes (`npm test`, `npm run lint`, `npm run build`, or the repo equivalent).".to_string());
-    }
-    if detection.tests_dir && detection.src_dir {
-        lines.push("- `src/` and `tests/` are both present; update both surfaces together when behavior changes.".to_string());
-    }
-    lines
-}
-
-fn repository_shape_lines(detection: &RepoDetection) -> Vec<String> {
-    let mut lines = Vec::new();
-    if detection.rust_dir {
-        lines.push(
-            "- `rust/` contains the Rust workspace and active CLI/runtime implementation."
-                .to_string(),
-        );
-    }
-    if detection.src_dir {
-        lines.push("- `src/` contains source files that should stay consistent with generated guidance and tests.".to_string());
-    }
-    if detection.tests_dir {
-        lines.push("- `tests/` contains validation surfaces that should be reviewed alongside code changes.".to_string());
-    }
-    lines
-}
-
-fn framework_notes(detection: &RepoDetection) -> Vec<String> {
-    let mut lines = Vec::new();
-    if detection.nextjs {
-        lines.push("- Next.js detected: preserve routing/data-fetching conventions and verify production builds after changing app structure.".to_string());
-    }
-    if detection.react && !detection.nextjs {
-        lines.push("- React detected: keep component behavior covered with focused tests and avoid unnecessary prop/API churn.".to_string());
-    }
-    if detection.vite {
-        lines.push("- Vite detected: validate the production bundle after changing build-sensitive configuration or imports.".to_string());
-    }
-    if detection.nest {
-        lines.push("- NestJS detected: keep module/provider boundaries explicit and verify controller/service wiring after refactors.".to_string());
-    }
-    lines
-}
-
-#[cfg(test)]
-mod tests {
-    use super::{initialize_repo, render_init_claude_md};
-    use std::fs;
-    use std::path::Path;
-    use std::time::{SystemTime, UNIX_EPOCH};
-
-    fn temp_dir() -> std::path::PathBuf {
-        let nanos = SystemTime::now()
-            .duration_since(UNIX_EPOCH)
-            .expect("time should be after epoch")
-            .as_nanos();
-        std::env::temp_dir().join(format!("rusty-claude-init-{nanos}"))
-    }
-
-    #[test]
-    fn initialize_repo_creates_expected_files_and_gitignore_entries() {
-        let root = temp_dir();
-        fs::create_dir_all(root.join("rust")).expect("create rust dir");
-        fs::write(root.join("rust").join("Cargo.toml"), "[workspace]\n").expect("write cargo");
-
-        let report = initialize_repo(&root).expect("init should succeed");
-        let rendered = report.render();
-        assert!(rendered.contains(".claude/         created"));
-        assert!(rendered.contains(".claude.json     created"));
-        assert!(rendered.contains(".gitignore       created"));
-        assert!(rendered.contains("CLAUDE.md        created"));
-        assert!(root.join(".claude").is_dir());
-        assert!(root.join(".claude.json").is_file());
-        assert!(root.join("CLAUDE.md").is_file());
-        assert_eq!(
-            fs::read_to_string(root.join(".claude.json")).expect("read claude json"),
-            concat!(
-                "{\n",
-                "  \"permissions\": {\n",
-                "    \"defaultMode\": \"acceptEdits\"\n",
-                "  }\n",
-                "}\n",
-            )
-        );
-        let gitignore = fs::read_to_string(root.join(".gitignore")).expect("read gitignore");
-        assert!(gitignore.contains(".claude/settings.local.json"));
-        assert!(gitignore.contains(".claude/sessions/"));
-        let claude_md = fs::read_to_string(root.join("CLAUDE.md")).expect("read claude md");
-        assert!(claude_md.contains("Languages: Rust."));
-        assert!(claude_md.contains("cargo clippy --workspace --all-targets -- -D warnings"));
-
-        fs::remove_dir_all(root).expect("cleanup temp dir");
-    }
-
-    #[test]
-    fn initialize_repo_is_idempotent_and_preserves_existing_files() {
-        let root = temp_dir();
-        fs::create_dir_all(&root).expect("create root");
-        fs::write(root.join("CLAUDE.md"), "custom guidance\n").expect("write existing claude md");
-        fs::write(root.join(".gitignore"), ".claude/settings.local.json\n")
-            .expect("write gitignore");
-
-        let first = initialize_repo(&root).expect("first init should succeed");
-        assert!(first
-            .render()
-            .contains("CLAUDE.md        skipped (already exists)"));
-        let second = initialize_repo(&root).expect("second init should succeed");
-        let second_rendered = second.render();
-        assert!(second_rendered.contains(".claude/         skipped (already exists)"));
-        assert!(second_rendered.contains(".claude.json     skipped (already exists)"));
-        assert!(second_rendered.contains(".gitignore       skipped (already exists)"));
-        assert!(second_rendered.contains("CLAUDE.md        skipped (already exists)"));
-        assert_eq!(
-            fs::read_to_string(root.join("CLAUDE.md")).expect("read existing claude md"),
-            "custom guidance\n"
-        );
-        let gitignore = fs::read_to_string(root.join(".gitignore")).expect("read gitignore");
-        assert_eq!(gitignore.matches(".claude/settings.local.json").count(), 1);
-        assert_eq!(gitignore.matches(".claude/sessions/").count(), 1);
-
-        fs::remove_dir_all(root).expect("cleanup temp dir");
-    }
-
-    #[test]
-    fn render_init_template_mentions_detected_python_and_nextjs_markers() {
-        let root = temp_dir();
-        fs::create_dir_all(&root).expect("create root");
-        fs::write(root.join("pyproject.toml"), "[project]\nname = \"demo\"\n")
-            .expect("write pyproject");
-        fs::write(
-            root.join("package.json"),
-            r#"{"dependencies":{"next":"14.0.0","react":"18.0.0"},"devDependencies":{"typescript":"5.0.0"}}"#,
-        )
-        .expect("write package json");
-
-        let rendered = render_init_claude_md(Path::new(&root));
-        assert!(rendered.contains("Languages: Python, TypeScript."));
-        assert!(rendered.contains("Frameworks/tooling markers: Next.js, React."));
-        assert!(rendered.contains("pyproject.toml"));
-        assert!(rendered.contains("Next.js detected"));
-
-        fs::remove_dir_all(root).expect("cleanup temp dir");
-    }
-}

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

@@ -1,4 +1,3 @@
-mod init;
 mod input;
 mod render;
 
@@ -21,7 +20,6 @@ use commands::{
     render_slash_command_help, resume_supported_slash_commands, slash_command_specs, SlashCommand,
 };
 use compat_harness::{extract_manifest, UpstreamPaths};
-use init::initialize_repo;
 use render::{Spinner, TerminalRenderer};
 use runtime::{
     clear_oauth_credentials, generate_pkce_pair, generate_state, load_system_prompt,
@@ -76,7 +74,6 @@ fn run() -> Result<(), Box<dyn std::error::Error>> {
             .run_turn_with_output(&prompt, output_format)?,
         CliAction::Login => run_login()?,
         CliAction::Logout => run_logout()?,
-        CliAction::Init => run_init()?,
         CliAction::Repl {
             model,
             allowed_tools,
@@ -109,7 +106,6 @@ enum CliAction {
     },
     Login,
     Logout,
-    Init,
     Repl {
         model: String,
         allowed_tools: Option<AllowedToolSet>,
@@ -234,7 +230,6 @@ fn parse_args(args: &[String]) -> Result<CliAction, String> {
         "system-prompt" => parse_system_prompt_args(&rest[1..]),
         "login" => Ok(CliAction::Login),
         "logout" => Ok(CliAction::Logout),
-        "init" => Ok(CliAction::Init),
         "prompt" => {
             let prompt = rest[1..].join(" ");
             if prompt.trim().is_empty() {
@@ -708,6 +703,26 @@ fn format_resume_report(session_path: &str, message_count: usize, turns: u32) ->
     )
 }
 
+fn format_init_report(path: &Path, created: bool) -> String {
+    if created {
+        format!(
+            "Init
+  CLAUDE.md        {}
+  Result           created
+  Next step        Review and tailor the generated guidance",
+            path.display()
+        )
+    } else {
+        format!(
+            "Init
+  CLAUDE.md        {}
+  Result           skipped (already exists)
+  Next step        Edit the existing file intentionally if workflows changed",
+            path.display()
+        )
+    }
+}
+
 fn format_compact_report(removed: usize, resulting_messages: usize, skipped: bool) -> String {
     if skipped {
         format!(
@@ -1097,7 +1112,7 @@ impl LiveCli {
                 false
             }
             SlashCommand::Init => {
-                run_init()?;
+                Self::run_init()?;
                 false
             }
             SlashCommand::Diff => {
@@ -1305,6 +1320,11 @@ impl LiveCli {
         Ok(())
     }
 
+    fn run_init() -> Result<(), Box<dyn std::error::Error>> {
+        println!("{}", init_claude_md()?);
+        Ok(())
+    }
+
     fn print_diff() -> Result<(), Box<dyn std::error::Error>> {
         println!("{}", render_diff_report()?);
         Ok(())
@@ -1522,7 +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,
     })
@@ -1667,26 +1688,50 @@ 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(),
+    append_memory_section(
+        &mut lines,
+        "Instruction files",
+        &project_context.instruction_files,
+        "No CLAUDE instruction files discovered in the current directory ancestry.",
     );
-    } else {
-        lines.push("Discovered files".to_string());
-        for (index, file) in project_context.instruction_files.iter().enumerate() {
+    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!("  {}. {}", index + 1, file.path.display()));
         lines.push(format!(
             "     lines={} preview={}",
             file.content.lines().count(),
@@ -1694,20 +1739,70 @@ fn render_memory_report() -> Result<String, Box<dyn std::error::Error>> {
         ));
     }
 }
-    Ok(lines.join(
-        "
-",
-    ))
-}
 
 fn init_claude_md() -> Result<String, Box<dyn std::error::Error>> {
     let cwd = env::current_dir()?;
-    Ok(initialize_repo(&cwd)?.render())
+    let claude_md = cwd.join("CLAUDE.md");
+    if claude_md.exists() {
+        return Ok(format_init_report(&claude_md, false));
     }
 
-fn run_init() -> Result<(), Box<dyn std::error::Error>> {
-    println!("{}", init_claude_md()?);
-    Ok(())
+    let content = render_init_claude_md(&cwd);
+    fs::write(&claude_md, content)?;
+    Ok(format_init_report(&claude_md, true))
+}
+
+fn render_init_claude_md(cwd: &Path) -> String {
+    let mut lines = vec![
+        "# CLAUDE.md".to_string(),
+        String::new(),
+        "This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.".to_string(),
+        String::new(),
+    ];
+
+    let mut command_lines = Vec::new();
+    if cwd.join("rust").join("Cargo.toml").is_file() {
+        command_lines.push("- Run Rust verification from `rust/`: `cargo fmt`, `cargo clippy --workspace --all-targets -- -D warnings`, `cargo test --workspace`".to_string());
+    } else if cwd.join("Cargo.toml").is_file() {
+        command_lines.push("- Run Rust verification from the repo root: `cargo fmt`, `cargo clippy --workspace --all-targets -- -D warnings`, `cargo test --workspace`".to_string());
+    }
+    if cwd.join("tests").is_dir() && cwd.join("src").is_dir() {
+        command_lines.push("- `src/` and `tests/` are also present; check those surfaces before removing or renaming Python-era compatibility assets.".to_string());
+    }
+    if !command_lines.is_empty() {
+        lines.push("## Verification".to_string());
+        lines.extend(command_lines);
+        lines.push(String::new());
+    }
+
+    let mut structure_lines = Vec::new();
+    if cwd.join("rust").is_dir() {
+        structure_lines.push(
+            "- `rust/` contains the Rust workspace and the active CLI/runtime implementation."
+                .to_string(),
+        );
+    }
+    if cwd.join("src").is_dir() {
+        structure_lines.push("- `src/` contains the older Python-first workspace artifacts referenced by the repo history and tests.".to_string());
+    }
+    if cwd.join("tests").is_dir() {
+        structure_lines.push("- `tests/` exercises compatibility and porting behavior across the repository surfaces.".to_string());
+    }
+    if !structure_lines.is_empty() {
+        lines.push("## Repository shape".to_string());
+        lines.extend(structure_lines);
+        lines.push(String::new());
+    }
+
+    lines.push("## Working agreement".to_string());
+    lines.push("- Prefer small, reviewable Rust changes and keep slash-command behavior aligned between the shared command registry and the CLI entrypoints.".to_string());
+    lines.push("- Do not overwrite existing CLAUDE.md content automatically; update it intentionally when repo workflows change.".to_string());
+    lines.push(String::new());
+
+    lines.join(
+        "
+",
+    )
 }
 
 fn normalize_permission_mode(mode: &str) -> Option<&'static str> {
@@ -2266,65 +2361,34 @@ fn convert_messages(messages: &[ConversationMessage]) -> Vec<InputMessage> {
         .collect()
 }
 
-fn print_help_to(out: &mut impl Write) -> io::Result<()> {
-    writeln!(out, "rusty-claude-cli v{VERSION}")?;
-    writeln!(out)?;
-    writeln!(out, "Usage:")?;
-    writeln!(
-        out,
-        "  rusty-claude-cli [--model MODEL] [--allowedTools TOOL[,TOOL...]]"
-    )?;
-    writeln!(out, "      Start the interactive REPL")?;
-    writeln!(
-        out,
-        "  rusty-claude-cli [--model MODEL] [--output-format text|json] prompt TEXT"
-    )?;
-    writeln!(out, "      Send one prompt and exit")?;
-    writeln!(
-        out,
-        "  rusty-claude-cli [--model MODEL] [--output-format text|json] TEXT"
-    )?;
-    writeln!(out, "      Shorthand non-interactive prompt mode")?;
-    writeln!(
-        out,
-        "  rusty-claude-cli --resume SESSION.json [/status] [/compact] [...]"
-    )?;
-    writeln!(
-        out,
-        "      Inspect or maintain a saved session without entering the REPL"
-    )?;
-    writeln!(out, "  rusty-claude-cli dump-manifests")?;
-    writeln!(out, "  rusty-claude-cli bootstrap-plan")?;
-    writeln!(
-        out,
-        "  rusty-claude-cli system-prompt [--cwd PATH] [--date YYYY-MM-DD]"
-    )?;
-    writeln!(out, "  rusty-claude-cli login")?;
-    writeln!(out, "  rusty-claude-cli logout")?;
-    writeln!(out, "  rusty-claude-cli init")?;
-    writeln!(out)?;
-    writeln!(out, "Flags:")?;
-    writeln!(
-        out,
-        "  --model MODEL              Override the active model"
-    )?;
-    writeln!(
-        out,
-        "  --output-format FORMAT     Non-interactive output format: text or json"
-    )?;
-    writeln!(
-        out,
-        "  --permission-mode MODE     Set read-only, workspace-write, or danger-full-access"
-    )?;
-    writeln!(out, "  --allowedTools TOOLS       Restrict enabled tools (repeatable; comma-separated aliases supported)")?;
-    writeln!(
-        out,
-        "  --version, -V              Print version and build information locally"
-    )?;
-    writeln!(out)?;
-    writeln!(out, "Interactive slash commands:")?;
-    writeln!(out, "{}", render_slash_command_help())?;
-    writeln!(out)?;
+fn print_help() {
+    println!("rusty-claude-cli v{VERSION}");
+    println!();
+    println!("Usage:");
+    println!("  rusty-claude-cli [--model MODEL] [--allowedTools TOOL[,TOOL...]]");
+    println!("      Start the interactive REPL");
+    println!("  rusty-claude-cli [--model MODEL] [--output-format text|json] prompt TEXT");
+    println!("      Send one prompt and exit");
+    println!("  rusty-claude-cli [--model MODEL] [--output-format text|json] TEXT");
+    println!("      Shorthand non-interactive prompt mode");
+    println!("  rusty-claude-cli --resume SESSION.json [/status] [/compact] [...]");
+    println!("      Inspect or maintain a saved session without entering the REPL");
+    println!("  rusty-claude-cli dump-manifests");
+    println!("  rusty-claude-cli bootstrap-plan");
+    println!("  rusty-claude-cli system-prompt [--cwd PATH] [--date YYYY-MM-DD]");
+    println!("  rusty-claude-cli login");
+    println!("  rusty-claude-cli logout");
+    println!();
+    println!("Flags:");
+    println!("  --model MODEL              Override the active model");
+    println!("  --output-format FORMAT     Non-interactive output format: text or json");
+    println!("  --permission-mode MODE     Set read-only, workspace-write, or danger-full-access");
+    println!("  --allowedTools TOOLS       Restrict enabled tools (repeatable; comma-separated aliases supported)");
+    println!("  --version, -V              Print version and build information locally");
+    println!();
+    println!("Interactive slash commands:");
+    println!("{}", render_slash_command_help());
+    println!();
     let resume_commands = resume_supported_slash_commands()
         .into_iter()
         .map(|spec| match spec.argument_hint {
@@ -2333,46 +2397,28 @@ fn print_help_to(out: &mut impl Write) -> io::Result<()> {
         })
         .collect::<Vec<_>>()
         .join(", ");
-    writeln!(out, "Resume-safe commands: {resume_commands}")?;
-    writeln!(out, "Examples:")?;
-    writeln!(
-        out,
-        "  rusty-claude-cli --model claude-opus \"summarize this repo\""
-    )?;
-    writeln!(
-        out,
-        "  rusty-claude-cli --output-format json prompt \"explain src/main.rs\""
-    )?;
-    writeln!(
-        out,
-        "  rusty-claude-cli --allowedTools read,glob \"summarize Cargo.toml\""
-    )?;
-    writeln!(
-        out,
-        "  rusty-claude-cli --resume session.json /status /diff /export notes.txt"
-    )?;
-    writeln!(out, "  rusty-claude-cli login")?;
-    writeln!(out, "  rusty-claude-cli init")?;
-    Ok(())
-}
-
-fn print_help() {
-    let _ = print_help_to(&mut io::stdout());
+    println!("Resume-safe commands: {resume_commands}");
+    println!("Examples:");
+    println!("  rusty-claude-cli --model claude-opus \"summarize this repo\"");
+    println!("  rusty-claude-cli --output-format json prompt \"explain src/main.rs\"");
+    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");
 }
 
 #[cfg(test)]
 mod tests {
     use super::{
-        filter_tool_specs, format_compact_report, format_cost_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,
-        normalize_permission_mode, parse_args, parse_git_status_metadata, print_help_to,
-        render_config_report, render_memory_report, render_repl_help,
-        resume_supported_slash_commands, status_context, CliAction, CliOutputFormat, SlashCommand,
-        StatusUsage, DEFAULT_MODEL,
+        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, normalize_permission_mode, parse_args,
+        parse_git_status_metadata, render_config_report, render_init_claude_md,
+        render_memory_report, render_repl_help, resume_supported_slash_commands, status_context,
+        CliAction, CliOutputFormat, SlashCommand, StatusUsage, DEFAULT_MODEL,
     };
     use runtime::{ContentBlock, ConversationMessage, MessageRole, PermissionMode};
-    use std::path::PathBuf;
+    use std::path::{Path, PathBuf};
 
     #[test]
     fn defaults_to_repl_when_no_args() {
@@ -2508,10 +2554,6 @@ mod tests {
             parse_args(&["logout".to_string()]).expect("logout should parse"),
             CliAction::Logout
         );
-        assert_eq!(
-            parse_args(&["init".to_string()]).expect("init should parse"),
-            CliAction::Init
-        );
     }
 
     #[test]
@@ -2666,11 +2708,12 @@ mod tests {
     }
 
     #[test]
-    fn init_help_mentions_direct_subcommand() {
-        let mut help = Vec::new();
-        print_help_to(&mut help).expect("help should render");
-        let help = String::from_utf8(help).expect("help should be utf8");
-        assert!(help.contains("rusty-claude-cli init"));
+    fn init_report_uses_structured_output() {
+        let created = format_init_report(Path::new("/tmp/CLAUDE.md"), true);
+        assert!(created.contains("Init"));
+        assert!(created.contains("Result           created"));
+        let skipped = format_init_report(Path::new("/tmp/CLAUDE.md"), false);
+        assert!(skipped.contains("skipped (already exists)"));
     }
 
     #[test]
@@ -2749,7 +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]
@@ -2774,7 +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);
     }
 
@@ -2832,7 +2875,7 @@ mod tests {
 
     #[test]
     fn init_template_mentions_detected_rust_workspace() {
-        let rendered = crate::init::render_init_claude_md(std::path::Path::new("."));
+        let rendered = render_init_claude_md(Path::new("."));
         assert!(rendered.contains("# CLAUDE.md"));
         assert!(rendered.contains("cargo clippy --workspace --all-targets -- -D warnings"));
     }

rust/crates/tools/src/lib.rs

@@ -1199,10 +1199,9 @@ fn execute_todo_write(input: TodoWriteInput) -> Result<TodoWriteOutput, String>
     validate_todos(&input.todos)?;
     let store_path = todo_store_path()?;
     let old_todos = if store_path.exists() {
-        serde_json::from_str::<Vec<TodoItem>>(
+        parse_todo_markdown(
             &std::fs::read_to_string(&store_path).map_err(|error| error.to_string())?,
-        )
-        .map_err(|error| error.to_string())?
+        )?
     } else {
         Vec::new()
     };
@@ -1220,10 +1219,7 @@ fn execute_todo_write(input: TodoWriteInput) -> Result<TodoWriteOutput, String>
     if let Some(parent) = store_path.parent() {
         std::fs::create_dir_all(parent).map_err(|error| error.to_string())?;
     }
-    std::fs::write(
-        &store_path,
-        serde_json::to_string_pretty(&persisted).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
@@ -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()