chore: cleanup Python remnants — docs, dead code, __pycache__

- CLAUDE.md: "Python, no native deps" → "single Rust binary"
- README/README_CN: "pure Python + Bash" → "single Rust binary + Bash skills"
- docs/flowctl.md: file structure updated to SQLite + YAML frontmatter
- Deleted cmd_task_set_section dead code (merged into task spec)
- Deleted __pycache__ in ralph templates
- Cleaned 13 Python JSON remnant files from .flow/

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: z23cc

CLAUDE.md

@@ -66,7 +66,7 @@ cd flowctl && cargo build --release && cargo test --all
 python3 -c "import json; json.load(open('hooks/hooks.json'))"
 ```
 
-No linter or formatter is configured. No TypeScript, no npm, no build step.
+Rust: clippy for linting, cargo test for tests. No TypeScript, no npm. Skills and agents are Markdown files (no build step).
 
 ## Key Design Decisions
 
@@ -97,7 +97,7 @@ No linter or formatter is configured. No TypeScript, no npm, no build step.
 - **Plan auto-execute**: `/flow-code:plan` defaults to auto-execute work after planning (≤10 tasks direct, >10 suggests Ralph); `--plan-only` to opt out
 - **Goal-backward verification**: worker Phase 5 re-reads acceptance criteria and verifies each is actually satisfied before completing
 - **Full-auto by default**: `/flow-code:plan` and `/flow-code:work` require zero interactive questions — AI reads git state, `.flow/` config, and request context to make branch, review, and research decisions autonomously. Default mode is Worktree + Teams + Phase-Gate (all three active). Work resumes from `.flow/` state on every startup (not a special "resume mode"). All tasks done → auto push + draft PR (`--no-pr` to skip)
-- **Cross-platform**: flowctl CLI works on macOS/Linux/Windows (Python, no native deps). RP plan-review auto-degrades to Codex on platforms where rp-cli is unavailable. Bash hooks degrade gracefully on Windows (skip, don't block)
+- **Cross-platform**: flowctl is a single Rust binary (macOS/Linux). RP plan-review auto-degrades to Codex on platforms where rp-cli is unavailable. Bash hooks degrade gracefully on Windows (skip, don't block)
 - **Session start**: CLAUDE.md instruction (not an enforced hook) — if `.flow/` exists, run `flowctl status --interrupted` to check for unfinished work from a previous session and resume with the suggested `/flow-code:work <id>` command
 
 ## Files to Never Commit
@@ -106,5 +106,5 @@ No linter or formatter is configured. No TypeScript, no npm, no build step.
 - `*.upstream` — upstream backup files
 - `.claude-plugin/` — local plugin config
 - `.tasks/` — runtime state
-- `__pycache__/` — Python cache
+- `__pycache__/` — Python cache (hook scripts only)
 - `.flow/` — per-project task state (runtime, not part of plugin)

README.md

@@ -37,7 +37,7 @@ A **harness** wraps around an AI coding agent to handle everything the model can
 | Full-auto (zero questions) | ✅ AI decides branch/review/depth | ❌ | ❌ | ❌ |
 | Context preservation | ✅ PreCompact hook | ❌ | ✅ embedding + RAG | ❌ |
 | Auto draft PR | ✅ | ❌ | ❌ | ❌ |
-| Zero dependencies | ✅ pure Python + Bash | ❌ Node.js | ❌ ChromaDB | ❌ Node.js |
+| Zero dependencies | ✅ single Rust binary + Bash skills | ❌ Node.js | ❌ ChromaDB | ❌ Node.js |
 
 ---
 
@@ -75,7 +75,7 @@ Flow-Code is a **harness engineering framework** for Claude Code. One command go
   → auto push + draft PR
 ```
 
-Everything lives in your repo as `.flow/` state. No external services. No global config. Zero dependencies (pure Python + Bash). Uninstall: delete `.flow/`.
+Everything lives in your repo as `.flow/` state. No external services. No global config. Single Rust binary + Bash skills. Uninstall: delete `.flow/`.
 
 <table>
 <tr>

README_CN.md

@@ -35,7 +35,7 @@
 | 运行时 DAG 变更 | ✅ 执行中 split/skip/dep rm | ❌ | ❌ | ❌ |
 | 跨模型对抗审查 | ✅ GPT 试图破坏 Claude 的代码 | ❌ | ❌ | ❌ |
 | 全自动（零问题） | ✅ AI 决定 branch/review/depth | ❌ | ❌ | ❌ |
-| 零依赖 | ✅ 纯 Python + Bash | ❌ Node.js | ❌ ChromaDB | ❌ Node.js |
+| 零依赖 | ✅ 单 Rust 二进制 + Bash 技能 | ❌ Node.js | ❌ ChromaDB | ❌ Node.js |
 
 ---
 
@@ -81,7 +81,7 @@ Flow-Code 是 Claude Code 的 **Harness Engineering 框架**。一条命令，
   → auto push + draft PR
 ```
 
-所有状态存储在 `.flow/` 目录。无外部服务。无全局配置。零依赖（纯 Python + Bash）。卸载：删除 `.flow/`。
+所有状态存储在 `.flow/` 目录。无外部服务。无全局配置。单 Rust 二进制 + Bash 技能。卸载：删除 `.flow/`。
 
 ---
 

docs/flowctl.md

@@ -26,23 +26,23 @@ Works out of the box for parallel branches. No setup required.
 ```
 .flow/
 ├── meta.json               # {schema_version, next_epic}
-├── epics/fn-N-slug.json    # Epic state (e.g., fn-1-add-oauth.json)
+├── epics/fn-N-slug.md      # Epic state (YAML frontmatter + markdown)
 ├── specs/fn-N-slug.md      # Epic spec (markdown)
-├── tasks/fn-N-slug.M.json  # Task state (e.g., fn-1-add-oauth.1.json)
-├── tasks/fn-N-slug.M.md    # Task spec (markdown)
-├── memory/                 # Agent memory (reserved)
-├── bin/                    # (optional) Local flowctl install via /flow-code:setup
-│   ├── flowctl
-│   ├── flowctl.py
-│   └── flowctl/           # Core engine package
-└── usage.md                # (optional) CLI reference via /flow-code:setup
+├── tasks/fn-N-slug.M.md    # Task state + spec (YAML frontmatter + markdown)
+├── memory/                 # Agent memory (v2 atomic entries)
+├── reviews/                # Review receipts (JSON)
+├── checklists/             # Machine-readable acceptance checklists
+└── .state/                 # SQLite DB (source of truth, in .git/flow-state/)
 ```
 
+Storage: SQLite is the authoritative store. Markdown files are the human-readable format.
+`flowctl import` rebuilds the DB from Markdown; `flowctl export` writes Markdown from DB.
+
 Flowctl accepts schema v1 and v2; new fields are optional and defaulted.
 
-New fields:
-- Epic JSON: `plan_review_status`, `plan_reviewed_at`, `completion_review_status`, `completion_reviewed_at`, `depends_on_epics`, `branch_name`, `default_impl`, `default_review`, `default_sync`, `gaps`
-- Task JSON: `priority`, `impl`, `review`, `sync`
+Frontmatter fields:
+- Epic: `plan_review`, `completion_review`, `depends_on_epics`, `branch_name`
+- Task: `priority`, `domain`, `depends_on`, `files`
 
 ## ID Format
 

flowctl/crates/flowctl-cli/src/commands/task/query.rs

@@ -1,4 +1,4 @@
-//! Task query and spec update commands: set-section, set-spec, set-backend, show-backend.
+//! Task query and spec update commands: set-spec, set-backend, show-backend.
 
 use chrono::Utc;
 use serde_json::json;
@@ -12,44 +12,6 @@ use super::{
     read_file_or_stdin, try_open_db, write_task_doc,
 };
 
-pub(super) fn cmd_task_set_section(json_mode: bool, task_id: &str, section: &str, file_path: &str) {
-    let flow_dir = ensure_flow_exists();
-
-    if !is_task_id(task_id) {
-        error_exit(&format!(
-            "Invalid task ID: {}. Expected format: fn-N.M or fn-N-slug.M",
-            task_id
-        ));
-    }
-
-    let mut doc = load_task_doc(&flow_dir, task_id);
-
-    // Read new content
-    let new_content = read_file_or_stdin(file_path);
-
-    // Patch body section
-    doc.body = patch_body_section(&doc.body, section, &new_content);
-    doc.frontmatter.updated_at = Utc::now();
-
-    write_task_doc(&flow_dir, task_id, &doc);
-
-    // Update DB
-    if let Some(conn) = try_open_db() {
-        let repo = flowctl_db::TaskRepo::new(&conn);
-        let _ = repo.upsert(&doc.frontmatter);
-    }
-
-    if json_mode {
-        json_output(json!({
-            "id": task_id,
-            "section": section,
-            "message": format!("Task {} {} updated", task_id, section),
-        }));
-    } else {
-        println!("Task {} {} updated", task_id, section);
-    }
-}
-
 pub(super) fn cmd_task_set_spec(
     json_mode: bool,
     task_id: &str,