Add full docs (diary, planning, cost tracking, entry format, philosophy) and refresh README

- Add comprehensive guides: docs/DIARY.md, docs/PLANNING.md, docs/COST_TRACKING.md, docs/ENTRY_FORMAT.md, docs/PHILOSOPHY.md
- Revise README to focus on journaling workflow, clarify Ollama vs Azure support, and streamline Quick Start/Usage sections
- Document logging behavior: file logs with rotation (10MB, 5 backups) and always-capture DEBUG to file; mention BRAIN_LOG_FILE and cost DB
- Simplify development/setup instructions and update examples for configuration and testing

Author: madebygps

README.md

@@ -2,7 +2,7 @@
 
 [![Tests](https://github.com/madebygps/second-brain/actions/workflows/test.yml/badge.svg)](https://github.com/madebygps/second-brain/actions/workflows/test.yml)
 
-AI-powered personal knowledge system with daily planning, reflective journaling, and semantic backlinks.
+AI-powered journaling with semantic backlinks. Extracts actionable tasks from reflections. Works with Azure OpenAI or local Ollama.
 
 ## Installation
 
@@ -44,242 +44,146 @@ uv run brain --help
 
 ## Features
 
-**Planning** (`brain plan`)
-- LLM extracts actionable tasks from yesterday's diary
-- Auto-carries forward unchecked todos from yesterday's plan
-- Saves to `PLANNER_PATH` with backlinks to source entries
+- **Morning planning** - LLM extracts tasks from yesterday's diary + carries forward uncompleted todos
+- **Evening reflection** - AI prompts based on your past 3 days
+- **Semantic backlinks** - LLM finds thematic connections (not keyword matching)
+- **Emotional patterns** - Tracks psychological themes over time
+- **Local or cloud** - Works with Ollama (free, private) or Azure OpenAI
+- **Obsidian-compatible** - Plain markdown with wiki-style links
 
-**Diary** (`brain diary`)
-- Evening reflection with AI-generated prompts from past 3 days
-- Semantic backlinks via LLM analysis (not keyword matching)
-- Automatic topic tags and temporal connections
-- Obsidian-compatible markdown format
-
-**Cost Tracking** (`brain cost`)
-- Real-time Azure OpenAI usage tracking in local SQLite database
-- Comprehensive metadata: temperature, max_tokens, prompt/response lengths
-- Summaries, trends, projections, and per-operation breakdowns
+**Documentation:**
+- [PHILOSOPHY.md](docs/PHILOSOPHY.md) - Design principles
+- [PLANNING.md](docs/PLANNING.md) - Planning guide
+- [DIARY.md](docs/DIARY.md) - Diary guide
+- [COST_TRACKING.md](docs/COST_TRACKING.md) - Cost tracking guide
 
 ## Quick Start
 
-### First-Time Setup
-
-1. **Install** (see [Installation](#installation) above)
-
-2. **Configure** - Create `~/.config/brain/.env` with your settings:
-
 ```bash
+# 1. Install
+uv tool install git+https://github.com/madebygps/second-brain.git
+
+# 2. Configure
 mkdir -p ~/.config/brain
 curl -o ~/.config/brain/.env https://raw.githubusercontent.com/madebygps/second-brain/main/.env.example
-nano ~/.config/brain/.env  # Edit with your paths and Azure credentials
+nano ~/.config/brain/.env  # Edit with your paths and LLM provider
+
+# 3. Use
+brain plan create today    # Morning: actionable tasks
+brain diary create today   # Evening: reflection
+brain diary link today     # Add semantic backlinks
 ```
 
-See [SETUP_CHECKLIST.md](SETUP_CHECKLIST.md) for detailed setup instructions.
+See [SETUP_CHECKLIST.md](SETUP_CHECKLIST.md) for detailed configuration.
 
-3. **Use**:
+## Usage
 
+**Daily workflow:**
 ```bash
-# Morning: Create your planning entry (saves to PLANNER_PATH)
-brain plan create today
-
-# Evening: Create your reflection entry (saves to DIARY_PATH)
-brain diary create today
+brain plan create today      # Morning planning
+brain diary create today     # Evening reflection
+brain diary link today       # Add semantic backlinks
 ```
 
-> **Note:** The `.env` file is automatically searched in `~/.config/brain/.env`, `~/.brain/.env`, or current directory.
->
-> **For developers:** When running locally, prefix commands with `uv run` (e.g., `uv run brain plan create today`)
-
-## Usage
-
+**Analysis:**
 ```bash
-# Planning
-brain plan create today        # Create daily plan with LLM task extraction
-brain plan create tomorrow     # Plan for tomorrow
-
-# Diary management
-brain diary create today       # Create reflection entry
-brain diary link today         # Generate semantic backlinks
-brain diary refresh 30         # Bulk refresh past 30 days
-brain diary list 7             # List recent entries
-
-# Analysis
-brain diary report 30          # Memory trace report (activities & connections)
-brain diary patterns 7         # Emotional & psychological patterns
-
-# Cost tracking and analysis
-brain cost summary             # Usage summary for last 30 days
-brain cost trends 30           # Daily cost trends
-brain cost estimate            # Monthly cost projection
-brain cost breakdown           # Per-operation breakdown
-brain cost export data.json    # Export to JSON
-brain cost pricing             # Show pricing
-
-# Logging (Rich-formatted, colored output)
-brain --verbose <command>      # Show key operations
-brain --debug <command>        # Full diagnostics with LLM details
+brain diary report 7         # Memory trace for past week
+brain diary patterns 7       # Emotional/psychological themes
+brain diary list            # List all entries
 ```
 
-> **Console Logs:** By default, logs are suppressed during operations to avoid interrupting spinners. Use `--verbose` or `--debug` for detailed information with beautiful Rich formatting.
+**Cost tracking** (Azure OpenAI only):
+```bash
+brain cost summary          # Usage stats
+brain cost trends 30        # Daily costs
+brain cost breakdown        # Per-operation costs
+```
 
-> **File Logs:** Optional. Set `BRAIN_LOG_FILE` in `.env` to enable persistent logging with automatic rotation (max 10MB per file, 5 backups). File logs always capture full DEBUG details regardless of console log level.
+**Debugging:**
+```bash
+brain --verbose <command>   # Show key operations
+brain --debug <command>     # Full diagnostics
+```
 
-> **Cost Tracking:** All Azure OpenAI usage is automatically tracked in a local SQLite database (`~/.brain/costs.db`). Data stays private and grows ~10-50 MB/year for typical use.
+Run `brain --help` for all commands.
 
 ## Configuration
 
-The `brain` CLI automatically searches for `.env` in these locations (in priority order):
-1. Current directory (`./.env`)
-2. User config directory (`~/.config/brain/.env`) ⭐ **Recommended**
-3. Home directory (`~/.brain/.env`)
-
-Create `~/.config/brain/.env` with these settings:
-
-**Required Paths:**
-- `DIARY_PATH` - Path to Obsidian vault or markdown directory for reflection entries
-- `PLANNER_PATH` - Path to directory for daily plan files (separate from diary)
-
-**LLM Provider** (choose one):
-- `LLM_PROVIDER` - Set to `azure` or `ollama` (default: `azure`)
-
-**Option 1: Azure OpenAI** (cloud-based, requires API key):
-- `AZURE_OPENAI_API_KEY` - Your Azure OpenAI API key
-- `AZURE_OPENAI_ENDPOINT` - Your Azure OpenAI endpoint
-- `AZURE_OPENAI_DEPLOYMENT` - Deployment name (default: `gpt-4o`)
-- `AZURE_OPENAI_API_VERSION` - API version (default: `2024-02-15-preview`)
-
-**Option 2: Ollama** (local, free, private):
-- `OLLAMA_BASE_URL` - Ollama API URL (default: `http://localhost:11434`)
-- `OLLAMA_MODEL` - Model name (default: `llama3.1`)
-- First install Ollama from https://ollama.com
-- Then pull a model: `ollama pull llama3.1`
-
-> **Switching Providers:** Just change `LLM_PROVIDER` in your `.env` file and restart. No code changes needed!
->
-> **Privacy:** Ollama runs completely locally. Your journal entries never leave your machine.
-
-**Logging & Cost Tracking** (optional configuration):
-- `BRAIN_COST_DB_PATH` - Path to cost tracking database (default: ~/.brain/costs.db)
-- `BRAIN_LOG_LEVEL` - Logging level: DEBUG, INFO, WARNING, ERROR (default: INFO)
-- `BRAIN_LOG_FILE` - Path to log file with automatic rotation (optional, logs to console if not set)
-  - When enabled: captures all DEBUG logs to file regardless of console log level
-  - Automatic rotation: max 10MB per file, keeps 5 backups (~50MB total)
-  - Example: `BRAIN_LOG_FILE=~/.brain/logs/brain.log`
-
-**Custom Pricing** (optional - override Azure OpenAI pricing):
-- `AZURE_GPT4O_INPUT_PRICE` - Price per 1K input tokens for gpt-4o (default: 0.03)
-- `AZURE_GPT4O_OUTPUT_PRICE` - Price per 1K output tokens for gpt-4o (default: 0.06)
-- `AZURE_GPT4O_MINI_INPUT_PRICE` - Price per 1K input tokens for gpt-4o-mini (default: 0.0015)
-- `AZURE_GPT4O_MINI_OUTPUT_PRICE` - Price per 1K output tokens for gpt-4o-mini (default: 0.006)
-- `AZURE_GPT4_INPUT_PRICE` - Price per 1K input tokens for gpt-4 (default: 0.03)
-- `AZURE_GPT4_OUTPUT_PRICE` - Price per 1K output tokens for gpt-4 (default: 0.06)
-- `AZURE_GPT35_TURBO_INPUT_PRICE` - Price per 1K input tokens for gpt-35-turbo (default: 0.0015)
-- `AZURE_GPT35_TURBO_OUTPUT_PRICE` - Price per 1K output tokens for gpt-35-turbo (default: 0.002)
+**Required:**
+```bash
+DIARY_PATH=/path/to/diary        # Reflection entries
+PLANNER_PATH=/path/to/planner    # Daily plans (separate)
+LLM_PROVIDER=ollama              # or "azure"
+```
 
-## Entry Format
+**Ollama** (local, free, private):
+```bash
+OLLAMA_BASE_URL=http://localhost:11434
+OLLAMA_MODEL=llama3.1
+```
 
-**Morning Plan Entry** (`YYYY-MM-DD-plan.md`):
+**Azure OpenAI** (cloud):
+```bash
+AZURE_OPENAI_API_KEY=your-key
+AZURE_OPENAI_ENDPOINT=https://your-resource.openai.azure.com/
+AZURE_OPENAI_DEPLOYMENT=gpt-4o
+```
 
-Saved to `PLANNER_PATH`. Created with `brain plan create`, which intelligently:
-- Extracts actionable tasks from yesterday's diary using LLM
-- Carries forward unchecked todos from yesterday's plan
-- Adds backlinks to source entries
+See [SETUP_CHECKLIST.md](SETUP_CHECKLIST.md) for full configuration options.
 
+## Entry Format
+
+**Morning Plan** (`YYYY-MM-DD-plan.md` in `PLANNER_PATH`):
 ```markdown
 ## Action Items
-- [ ] Follow up with team about project (from [[2025-01-14]])
-- [ ] Review pull requests (from [[2025-01-14]])
-- [ ] Uncompleted task from yesterday (from [[2025-01-14]])
+- [ ] Task from yesterday's diary (from [[2025-10-14]])
+- [ ] Unchecked task from yesterday's plan (from [[2025-10-13-plan]])
 ```
 
-**Evening Reflection Entry** (`YYYY-MM-DD.md`):
-
-Saved to `DIARY_PATH`. Created with `brain diary create`:
-
+**Evening Reflection** (`YYYY-MM-DD.md` in `DIARY_PATH`):
 ```markdown
 ## Reflection Prompts
-**1. Based on [[2025-01-14]], how did X work out?**
+**1. AI-generated prompt based on past 3 days**
 
 ---
 
 ## Brain Dump
-Your reflections...
-```
-
-After writing, run `brain diary link today` to add semantic backlinks:
+Your free-form reflection...
 
-```markdown
 ---
 
 ## Memory Links
-**Temporal:** [[2025-01-14]] • [[2025-01-13]]
-**Topics:** #focus #energy
+[Generated by: brain diary link today]
+**Temporal:** [[2025-10-14]] • [[2025-10-13]]
+**Topics:** #self-doubt #growth #perfectionism
 ```
 
+See [ENTRY_FORMAT.md](docs/ENTRY_FORMAT.md) for quick reference.
+
 ## Requirements
 
 - Python 3.13+
-- uv package manager (ALWAYS use `uv`, never `pip`)
-- **LLM Provider** (choose one):
-  - **Azure OpenAI** - Cloud-based, requires API key and subscription
-  - **Ollama** - Local, free, completely private (requires installation from https://ollama.com)
-- All LLM features supported with either provider:
-  - Diary prompt generation
-  - Task extraction from diary entries
-  - Semantic backlinks and tags
-  - Analysis reports and patterns
+- uv package manager
+- LLM Provider (choose one):
+  - **Ollama** - Local, free, private ([install](https://ollama.com))
+  - **Azure OpenAI** - Cloud, requires API key
 
 ## Development
 
-### Testing
-
-Minimal test suite focused on preventing data loss:
-
 ```bash
-uv run pytest                    # Run all tests
-uv run pytest --cov              # Run with coverage
-```
-
-**Coverage**: 7 essential tests covering:
-- Configuration validation (missing paths)
-- File naming (reflection vs. plan entries)
-- Write/read cycles (prevent data loss)
-- Path separation (diary vs. planner)
-
-### Code Quality
-
-Pre-commit hooks automatically run before each commit:
-
-```bash
-# Install hooks (one-time setup)
-uv run pre-commit install
-
-# Run manually on all files
-uv run pre-commit run --all-files
+git clone https://github.com/madebygps/second-brain.git
+cd second-brain
+uv sync                          # Install dependencies
+uv run pre-commit install        # Setup hooks
+cp .env.example .env             # Configure
+uv run brain --help              # Test
+
+# Testing
+uv run pytest                    # Run tests
+uv run pytest --cov              # With coverage
 ```
 
-**Hooks include:**
-- `ruff` - Fast Python linter with auto-fix
-- `ruff-format` - Auto-format Python code
-- `pytest` - Run test suite (prevents data loss bugs)
-- File checks (trailing whitespace, file endings, large files)
-
-**[pre-commit.ci](https://pre-commit.ci) integration:**
-- ✅ Automatically fixes PRs (formatting, imports, etc.)
-- ✅ Weekly dependency updates
-- ✅ Zero configuration needed
-
-### CI/CD
-
-**GitHub Actions** runs on push/PR:
-- ✅ Tests with coverage reporting
-- ✅ Test count validation (ensures 7 tests)
-- ✅ Python 3.13 compatibility check
-
-**[pre-commit.ci](https://pre-commit.ci)** runs on PRs:
-- ✅ Auto-fixes formatting and linting issues
-- ✅ Weekly dependency updates (automated PRs)
-- ✅ Faster than GitHub Actions for simple checks
+See [PHILOSOPHY.md](docs/PHILOSOPHY.md) for architecture and design decisions.
 
 ## License