Update documentation for web-first architecture

- Remove CLI command docs (query, report, interact, explore) - now web-only
- Simplify CLI docs to just launching the server (serve is now optional)
- Rename sections to match UI: Interface, Monitor, Insights, Explore
- Reorder Interface subsections to match actual UI navigation
- Document new Access Denied alert type
- Update Explore page to describe structured query tabs and Query tab
- Add access, access_old, access_new columns to Query Syntax
- Add schedule_id, size_old, size_new columns to Query Syntax
- Reorder Query Syntax columns to match database schema
- Fix code block annotations to pass mdbook test

Author: gtunes-dev

README.md

@@ -56,7 +56,7 @@ Whether you're managing storage capacity, tracking project evolution, or ensurin
 - **Historical Analysis** — Interactive trend charts show how your data evolves: sizes, counts, changes, and alerts
 - **Alert System** — Suspicious hash changes and validation failures flagged immediately with status management
 - **Powerful Query Language** — SQL-inspired syntax for filtering, sorting, and analyzing your filesystem data
-- **Dual Interface** — Elegant web UI for visual exploration, full-featured CLI for automation and scripting
+- **Web-First Design** — Elegant web UI for all operations including scanning, browsing, querying, and configuration
 
 ---
 
@@ -68,10 +68,9 @@ Quick start instructions are below, but full documentation is available in book
 
 Key sections:
 - [Getting Started](https://gtunes-dev.github.io/fspulse/getting_started.html) — Installation, Docker deployment, and first steps
-- [Web Interface](https://gtunes-dev.github.io/fspulse/web_ui.html) — Complete guide to Monitor, Browse, Insights, Alerts, and Explore pages
+- [Interface](https://gtunes-dev.github.io/fspulse/web_ui.html) — Complete guide to Monitor, Browse, Insights, Alerts, and Explore pages
 - [Scanning Concepts](https://gtunes-dev.github.io/fspulse/scanning.html) — How scans work, hashing, and validation
 - [Query Syntax](https://gtunes-dev.github.io/fspulse/query.html) — Powerful filtering and data exploration
-- [Command-Line Interface](https://gtunes-dev.github.io/fspulse/cli.html) — CLI commands for automation and scripting
 - [Configuration](https://gtunes-dev.github.io/fspulse/configuration.html) — Customizing FsPulse behavior
 
 ---
@@ -93,69 +92,53 @@ The [Docker Deployment Guide](https://gtunes-dev.github.io/fspulse/docker.html)
 
 ---
 
-## ⚡ Usage Examples
+## ⚡ Running FsPulse
 
-FsPulse can run in three modes depending on your needs:
-
-### Web UI Mode
-
-Start the server and access through your browser:
+Start the FsPulse server:
 
 ```sh
-fspulse serve
+fspulse
 ```
 
-Open **http://127.0.0.1:8080** in your browser to access the full web interface.
-
-**Great for:** Visual data exploration, managing multiple roots, real-time scan monitoring, continuous awareness
-
----
-
-### Command-Line Mode
-
-Direct terminal commands for scripting and automation:
+Or explicitly:
 
 ```sh
-# Query for invalid items
-fspulse query "items where val:(I)"
-
-# View recent scans
-fspulse report scans --last 5
-
-# Find items with hash changes
-fspulse query "changes where hash_change:(T) show item_path, hash_old, hash_new"
-
-# Find directories over 10GB
-fspulse query "items where size > 10GB and item_type:(D)"
+fspulse serve
 ```
 
-**Great for:** Automation, scripted workflows, CI/CD integration, quick one-off operations
-
-**Note:** All scanning is performed through the web UI. The CLI provides powerful querying and reporting capabilities.
+Open **http://127.0.0.1:8080** in your browser to access the web interface.
 
----
+All functionality is available through the web UI:
+- Configure and manage scan roots
+- Schedule automatic scans
+- Monitor scan progress in real-time
+- Browse your filesystem hierarchy
+- Query and explore your data
+- Manage alerts and validation issues
 
-### Interactive Terminal Mode
+### Configuration
 
-Menu-driven interfaces for guided terminal workflows:
+FsPulse is configured through environment variables or a config file:
 
 ```sh
-fspulse interact  # Menu-driven interface
-fspulse explore   # Full-screen data explorer
+# Example: Change port and enable debug logging
+export FSPULSE_SERVER_PORT=9090
+export FSPULSE_LOGGING_FSPULSE=debug
+fspulse
 ```
 
-**Great for:** Terminal users who want visual feedback without leaving the command line
+See the [Configuration Guide](https://gtunes-dev.github.io/fspulse/configuration.html) for all available settings.
 
 ---
 
-### 🖥️ Web Interface Highlights
+### 🖥️ Interface Highlights
 
-The web UI provides powerful visual tools for monitoring and exploring your data:
+The interface provides powerful visual tools for monitoring and exploring your data:
 
-- **Monitor & Schedule** — Configure automatic scans with flexible scheduling options, view execution queue status, and manage scan roots
+- **Monitor** — Configure automatic scans with flexible scheduling options, view execution queue status, and manage scan roots
 - **Live Scan Progress** — Watch scan activity in real-time whether manually initiated or scheduled, with detailed phase-by-phase statistics
 - **Browse with Detail View** — Explore your filesystem hierarchy with elegant sliding panels showing item metadata, validation status, alerts, and complete change history
-- **Insights & Trends** — Interactive charts tracking file sizes, counts, change activity, and validation issues over time with customizable date ranges
+- **Insights** — Interactive charts tracking file sizes, counts, change activity, and validation issues over time with customizable date ranges
 - **Alert Management** — Filter, flag, and dismiss integrity issues with context-aware views and status tracking
 
 <p align="center">

docs/book.toml

@@ -1,6 +1,5 @@
 [book]
 authors = ["gtunes-dev"]
 language = "en"
-multilingual = false
 src = "src"
 title = "FsPulse"

docs/src/SUMMARY.md

@@ -7,17 +7,14 @@
   - [Docker Deployment](docker.md)
   - [First Steps](getting_started/first_steps.md)
 - [Scanning Concepts](scanning.md)
-- [Web Interface](web_ui.md)
+- [Interface](web_ui.md)
   - [Scans](web_ui/scans.md)
-  - [Monitor & Scheduling](web_ui/monitor.md)
+  - [Monitor](web_ui/monitor.md)
   - [Browse](web_ui/browse.md)
-  - [Insights & Trends](web_ui/insights.md)
   - [Alerts](web_ui/alerts.md)
-  - [Explore (Query Interface)](web_ui/explore.md)
+  - [Insights](web_ui/insights.md)
+  - [Explore](web_ui/explore.md)
 - [Command-Line Interface](cli.md)
-  - [Query Command](cli/query.md)
-  - [Report Commands](cli/reports.md)
-  - [Interactive Mode](interactive_mode.md)
 - [Query Syntax](query.md)
 - [Configuration](configuration.md)
 - [Validators](validators.md)

docs/src/cli.md

@@ -1,58 +1,83 @@
 # Command-Line Interface
 
-FsPulse is designed with the web UI as the primary interface for all users. However, the CLI provides powerful capabilities for expert users who prefer terminal workflows, automation, and scripting integration.
+FsPulse is a **web-first application**. The CLI exists solely to launch the web server—all functionality including scanning, querying, browsing, and configuration is accessed through the [Interface](web_ui.md).
 
-## CLI Purpose and Limitations
+---
+
+## Starting FsPulse
+
+To start the FsPulse server:
+
+```sh
+fspulse
+```
+
+Or explicitly:
+
+```sh
+fspulse serve
+```
 
-**What the CLI Provides:**
-- Query and analyze scan data
-- Generate formatted reports
-- Automate data analysis workflows
-- Integrate with scripts, cron jobs, and CI/CD pipelines
+Both commands are equivalent. The server starts on `http://127.0.0.1:8080` by default.
 
-**Important Limitation:**
-All **scanning operations** must be performed through the web UI. Start the server with `fspulse serve` and use the [Web Interface](web_ui.md) to configure and run scans. The CLI provides access to query and analyze data generated by scans, but cannot initiate scans.
+Once running, open your browser to access the full web interface for:
+- Managing scan roots and schedules
+- Running and monitoring scans
+- Browsing your filesystem data
+- Querying and exploring results
+- Managing alerts
 
 ---
 
-## Available Commands
+## Configuration
 
-### Data Analysis
+FsPulse behavior is configured through **environment variables** or a **config file**, not command-line flags.
 
-- **[query](cli/query.md)** — Execute SQL-inspired queries against scan data
-- **[report](cli/reports.md)** — Generate prebuilt formatted reports
+### Environment Variables
 
-### Interactive Interfaces
+Set these before running `fspulse`:
 
-- **[interact / explore](interactive_mode.md)** — Menu-driven and full-screen TUI interfaces for terminal users
+```sh
+# Server settings
+export FSPULSE_SERVER_HOST=0.0.0.0    # Bind address (default: 127.0.0.1)
+export FSPULSE_SERVER_PORT=9090       # Port number (default: 8080)
+
+# Analysis settings
+export FSPULSE_ANALYSIS_THREADS=16    # Worker threads (default: 8)
+
+# Logging
+export FSPULSE_LOGGING_FSPULSE=debug  # Log level (default: info)
 
-### Server
+# Data location
+export FSPULSE_DATA_DIR=/custom/path  # Data directory override
+
+fspulse
+```
 
-- **serve** — Start the FsPulse web service (default: `http://127.0.0.1:8080`)
+### Configuration File
+
+FsPulse also reads from `config.toml` in the data directory. See [Configuration](configuration.md) for complete documentation including:
+- All available settings
+- Environment variable reference
+- Platform-specific data directory locations
+- Docker configuration
 
 ---
 
 ## Getting Help
 
-View available commands and options:
+View version and basic usage:
 
 ```sh
 fspulse --help
-fspulse <command> --help
-```
-
-Examples:
-```sh
-fspulse query --help
-fspulse report scans --help
+fspulse --version
 ```
 
 ---
 
 ## Related Documentation
 
-- **[Query Syntax](query.md)** — Learn the query language used by the `query` command
-- **[Configuration](configuration.md)** — Configure database location, server settings, and more
-- **[Web Interface](web_ui.md)** — Primary interface for all users including scan management
-- **[Docker Deployment](docker.md)** — Using CLI commands in Docker containers
+- **[Configuration](configuration.md)** — Complete configuration reference
+- **[Interface](web_ui.md)** — Guide to all UI features
+- **[Docker Deployment](docker.md)** — Running FsPulse in Docker