宜博 / lemonboss

- Fixed .gitignore: data/system/ prefix was missing (old paths never matched)
- Removed tracked memory/, conversations/, uploads/, .tasks/ files
- Only memory.md and hippocampus.md are kept (template skeleton)

- Added inline editing for template description and type fields
- Implemented Delete Template functionality (removes both file system and registry entry)
- Added confirmation safeguards for the destructive delete action

Architecture fix for long-running tool execution:

1. ClaudeCliProtocol: Two-tier idle timeout
   - Chat mode: 45s (detect API hang/silent rate limit)
   - Tool execution mode: 5min (Bash long tasks like pip install)
   - Automatically switches on tool_use_start / content_block_stop events

2. Provision API: POST /templates/:templateId/provision
   - Runs shell commands directly via child_process.exec
   - Bypasses Claude ACP entirely (no idle timeout issue)
   - 10min per-command timeout, security blocklist
   - Frontend button with prompt for custom commands

3. Template UI: Added 🔧 安装依赖 button (teal)

Fixed 4 hidden bugs where path.join(DATA_ROOT, "system", ...) was used instead
of direct path.resolve to root-level system/:

- agent-chat.js: billing log scan (line 804) and agent list scan (line 909)
- company-service.js: TEMPLATES_DIR and GLOBAL_AGENTS_DIR constants
- heartbeat-service.js: system agents scan directory

These were missed because they used path.join with a variable (DATA_ROOT)
rather than the literal string "data/system" that sed caught.

- Moved data/system/ → system/ (agents, templates, skills, data, workspace)
- Updated all server route/service path references
- Updated all script path references
- Updated all documentation references
- Restructured .gitignore for cleaner system/ vs data/ boundary

system/ = platform-shared assets (system agents, template library)
data/ = tenant-specific company instance data

…aruncreate skill paths

- Upload skill files to .claude/skills/ (Claude Code ACP reads from here)
- Add conversation type filter (user/callback/task/train) to AgentChat
- Parse messages.log for richer conversation history display
- Fix idearuncreate template & company agent skill directory structure
- Add adm-zip dependency for ZIP extraction
- Add fs/path top-level requires in company.js

# Conflicts:
#	data/system/agents/agent-creator/memory/memory.md
#	data/system/agents/innovator/memory/hippocampus-index.json
#	data/system/agents/innovator/memory/hippocampus.md
#	data/system/agents/innovator/memory/memory.md
#	data/system/agents/master/memory/cerebellum/task-callback.md
#	data/system/agents/master/memory/hippocampus-index.json
#	data/system/agents/master/memory/hippocampus.md
#	data/system/agents/master/memory/memory.md

- Add TaskTimeline.vue: two-pane dashboard with task list + message timeline
- Add task-service.js: aggregate cross-agent conversations into task tree
  - 4-strategy parent-child inference (explicit meta, time-overlap, conv→tpl, master→T)
  - Read messages.log for full tool call details (not just history.json)
- Add tasks.js API routes: GET /api/tasks, GET /api/tasks/:taskId/timeline
- Mount /api/tasks in agent-server.js
- Add 'Task Logs' nav entry in AppNav.vue after Templates
- Support taskId in URL (/tasks/:taskId?) for sharing/bookmarking
- Add --parent flag to CLI task dispatch for explicit parentTaskId
- Auto-detect parentTaskId in task/dispatch from sender's active task
- Add --instructions flag to template train CLI command
- Update master tools.md with new parameters

…ictly enforce empty shell company creation

…th time-based multi-dimension token tracking charts

…en costs across agents

- Updated `GET /api/agent/:agentId/info` to include heartbeat and cron configurations.
- Added `PUT /api/agent/:agentId/heartbeat` to update config.json and toggle service heartbeat on the fly.
- Added `PUT /api/agent/:agentId/cron` to update cron.json list.
- Updated AgentChat.vue detail panel UI to include interactive heartbeat toggles and a cron job management list.

- Updated `POST /api/company/create` to create an empty shell without bootstrapping CXO/HR automatically.
- Updated `master/agent.md` instructions so Master Agent handles all Template library hirings.
- Renamed 'MasterBot' navigation link to 'System Agents'.
- Updated AgentChat sidebar to only show System Agents when accessed via the System Agents link.

Copy innovator pipeline agents from templates/ to system/agents/:
- agent-creator: scaffolds new agents
- innovator: orchestrates FDE training pipeline
- hunter: knowledge hunting (L3-Hunt)
- digester: knowledge digestion (L2-Digest)
- evolver: skill evolution (Evolving)

All 6 system agents now visible in MasterBot agent list.

- GET /api/company/templates/:id/logs scans system agent conversations
- Logs stored in system agents (agent-creator/innovator), NOT in template dir
- Template directories stay clean for copying
- Collapsible log cards with status, time, message count, and output summary
- Auto-poll during generate/train actions (10s/15s intervals)

- POST /api/company/templates: scaffold new template via AgentScaffold
- POST /api/company/templates/:id/generate: trigger agent-creator to write definitions
- POST /api/company/templates/:id/train: trigger innovator FDE training pipeline
- PUT /api/company/templates/:id/files/content: save template file content
- TemplateAgents.vue: create form, action buttons, editable preview, status banner

- Chat list: added 🗑 delete button per conversation (hover to reveal)
  - Calls DELETE /api/agent/:agentId/conversations/:convId
  - Backend also cleans up associated log files
- Detail file tree: added 🗑 delete button per file/folder (hover to reveal)
  - Backend: DELETE /api/agent/:agentId/file/* with path traversal protection
- Detail preview: upgraded from readonly <pre> to editable <textarea>
  - Backend: PUT /api/agent/:agentId/file/* for saving
  - Shows 'unsaved' badge + save/reset buttons when dirty
  - Tab key support, monospace font, auto-fill height

- CompanyDashboard Goals Tab: upgraded from flat list to full OKR tree view
  with progress bars, node hierarchy, status animations, owner/priority badges
- ClaudeCliProtocol: added --effort flag support (low=disable thinking)
- agent-chat.js: per-agent effort config from config.json cli.effort
- .gitignore: exclude data/companies/, apiconversation/, agent memory/tasks
- New views: TemplateAgents, JobsPanel, PipelineEditor, SkillsMarket
- docs/architecture-v5.md: added decision #13 (thinking control)

1. 根治所有模板 Agent残留的过往公司(LemonV)私人记忆，使其诞生即为全新白纸状态。
2. 提取出统一的 `methodology.md` 基类 Prompt，通过 `agent-chat.js` 强力注入。
3. 从 Master 到各路 Agent 都将强制遵循【从大脑到小脑】的不硬编码理念。
4. 全面引入统一的基础方法论（Harness）：学习(Research) -> 规划(Planning) -> 执行(Execute) -> 验证(Verify)

- 移除了 master/agent.md 中关于自动部署 CEO/CTO/COO/HR 的错误硬编码约定
- 更新了 master/tools.md 工作流，明确 Master 第一步需手动 hire CEO 并派发战略指令
- 清理了 templates/ceo 下自带的、绑定具体公司的 plan.md 和 todo.md 假数据模板，确保 CEO 诞生时是一张白纸