think-bigger/docs/grok-chat/Functional Specification: Advanced.md

Functional Specification: Advanced Second Brain PKM System

This document outlines the core functional requirements and features for the Advanced Second Brain Personal Knowledge Management (PKM) system, derived from the detailed UI design proposal. The system is designed to be a highly advanced "Second Brain" that integrates local data sovereignty with a multi-agent hierarchical architecture.

1. Core System Capabilities

The foundation of the PKM system rests on four critical capabilities that define its advanced nature and functionality. These capabilities ensure the system is both a powerful knowledge repository and a flexible development environment.

Feature	Description	Technical Requirement
Local Data Sovereignty	All domain-specific knowledge, metadata, knowledge graphs, and embeddings must be linked to and stored in a singular, local directory on the user's system. This ensures user control and ownership of all data assets.	File system integration, secure local storage, and directory monitoring capabilities.
Multi-Agent Architecture	The system must support the deployment and management of multiple domain-specific agents, each functioning as an expert in its chosen field of knowledge.	A robust agent orchestration layer is required to manage agent lifecycle and communication, with native integration for the Dana language.
Dana Language Integration	The system must natively support the Dana language for defining and executing agent logic, including features for editing, testing, and real-time execution.	Requires a Dana compiler or interpreter, along with a fully functional Read-Eval-Print Loop (REPL) environment integrated into the application.
Knowledge Graph/Embeddings	Each domain must utilize a dynamic knowledge graph and associated vector embeddings for advanced semantic querying, context management, and relationship visualization.	Integration with a suitable graph database and an efficient embedding generation pipeline are necessary.

2. View-Specific Features

The application is structured around four primary views, each tailored to a specific user interaction pattern: global navigation, dashboard overview, domain-specific knowledge work, and cross-domain orchestration.

2.1. Global Navigation (Persistent Sidebar)

A narrow, persistent sidebar serves as the primary anchoring element on the far left of every screen. This sidebar provides immediate access to the highest-level views and facilitates rapid context switching. The core links include the Dashboard / Goals ([🏠]), the Global Orchestrator Chat ([💬]), and Settings / Data Map ([⚙️]). Below these core links, a Domain Quick Switch section lists all configured knowledge domains (e.g., [🧠] Neuroscience, [💻] CompSci), allowing the user to switch contexts instantly. The sidebar also includes a link for Domain Management ([➕] Add Domain) and a User Profile link ([👤]).

2.2. View 1: The Dashboard (Home Base)

The Dashboard is the user's landing page, providing a high-level overview of personal objectives and the current state of the knowledge landscape. Its layout is divided into two main columns. The Left Column is dedicated to Goals & Status, featuring a Personal Objectives Module (functioning as a checklist or Kanban board for tracking learning goals) and a System Status display that provides real-time updates on background processes (e.g., "Orchestrator: Idle," "Scraper Agent: Active"). The Right Column presents the Domain Grid, a collection of large, clickable cards for each domain. Each card must display the domain icon, name, document count, last active date, and a small status indicator reflecting the health and training status of its specific Dana Agent (e.g., "Agent Status: Trained").

2.3. View 2: Domain Workspace - Knowledge Browser Mode

This is the core reading and analysis view, designed to manage data density through a three-pane layout. A sub-navigation bar at the top allows switching between the Knowledge Browser, Agent Studio (Dana IDE), and Domain Settings.

The three main panes are:

1. Pane 1: The Drawer (Far Left): This pane displays a file tree that mirrors the local domain directory structure, including categories like 📁 Papers, 📁 Notes, 📹 Media, and 🕸️ Scraped_Web. Its primary function is to act as a source selector; clicking any file loads its content into the Middle Pane.
2. Pane 2: Content Viewer (Middle): This is the largest, most flexible pane, dedicated to content display. For text and PDF files, it must provide a robust, clean reading experience with a high-fidelity renderer. For video content, it must feature a video player synchronized with an interactive transcript displayed below, allowing users to navigate the video by clicking text.
3. Pane 3: Insight/Fabric (Right): This pane is initially blank but contains a [ Run Fabric Pattern ] button. Its function is to generate structured output based on selected "Fabric" analysis patterns (e.g., "Extract Wisdom," "Summarize," "Find Action Items") against the content currently displayed in the Content Viewer.

An Ubiquitous Chat Overlay—a floating chat bubble at the bottom right—provides immediate, context-aware access to the domain agent for questions specifically related to the currently open document and domain.

2.4. View 3: Domain Workspace - Agent Studio Mode (Dana IDE)

The Agent Studio is an IDE-style environment for engineering and customizing the domain's Dana agent. It is divided into three functional areas:

1. Left Panel (Context & Graph Manager): This area manages the agent's knowledge sources. It includes a checklist of file paths that define the agent's context and a Visualizer—a mini-map of the domain's knowledge graph. The visualizer must allow users to click a node to highlight relevant code or source documents.
2. Middle Panel (The Dana Editor): This is a full-featured code editor with syntax highlighting for Dana. It must support tabbed editing for core agent files such as agent.dana, tools.dana, and config.json.
3. Bottom Panel (The REPL & Logs): This panel provides an interactive Terminal for the Dana REPL, enabling immediate testing of agent functions (e.g., dana> load agent.dana). It also displays real-time Logs for agent indexing, execution, and error reporting.

2.5. View 4: Global Orchestrator Chat

The Global Orchestrator Chat is a large, central chat interface designed for complex, cross-domain querying. Its distinguishing feature is the Domain Scope Selector, located just above the chat input bar. This selector allows the user to explicitly choose which knowledge bases/domains are relevant to the query using checkboxes (e.g., [x] History, [x] Economics). The backend's core functionality here is to intelligently determine whether to call individual domain agents and synthesize their answers or handle the query with the orchestrator alone, displaying the resulting synthesis in the Chat History.