Add user manual documenting non-obvious features and shortcuts

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: ozgesolidkey

MANUAL.md

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+# LOGAN User Manual
+
+## Keyboard Shortcuts
+
+### Files & Tabs
+| Shortcut | Action |
+|----------|--------|
+| Ctrl+O | Open file |
+| Ctrl+T | New tab |
+| Ctrl+W | Close tab |
+| Ctrl+Tab | Next tab |
+| Ctrl+Shift+Tab | Previous tab |
+| Drag & drop | Drop files or folders into window to open |
+
+### Navigation
+| Shortcut | Action |
+|----------|--------|
+| Arrow Up/Down | Move one line |
+| Page Up/Down | Move by page |
+| Home / End | Jump to first / last line |
+| Arrow Left/Right | Scroll horizontally |
+| Shift+Scroll wheel | Horizontal scroll |
+
+### Search
+| Shortcut | Action |
+|----------|--------|
+| Ctrl+F | Focus search box |
+| Enter | Run search |
+| F3 / Ctrl+G | Next result |
+| Shift+F3 / Ctrl+Shift+G | Previous result |
+| Ctrl+Shift+R | Toggle search results panel |
+
+### Bookmarks & Highlights
+| Shortcut | Action |
+|----------|--------|
+| Ctrl+B | Toggle bookmark on current line |
+| Ctrl+H | Highlight selected text (all occurrences) |
+| Ctrl+Shift+H | Highlight selected text (first per line) |
+| Ctrl+Shift+S | Save selected lines as snippet to notes file |
+
+### Panels
+| Shortcut | Action |
+|----------|--------|
+| Ctrl+1 | Folders |
+| Ctrl+2 | Bookmarks |
+| Ctrl+3 | Highlights |
+| Ctrl+4 | Statistics |
+| Ctrl+5 | History |
+| Ctrl+6 | Analysis (bottom) |
+| Ctrl+7 | Time Gaps (bottom) |
+| Ctrl+8 | Search Configs (bottom) |
+| Ctrl+9 | Video Sync (bottom) |
+| Ctrl+Shift+P | Live connections panel |
+| Ctrl+\\ | Toggle panel visibility |
+| Escape | Close active panel or modal |
+
+### Special
+| Shortcut | Action |
+|----------|--------|
+| Ctrl+\` | Terminal (drop-down from top) |
+| Ctrl+Shift+N | Notes drawer (slide-up from bottom) |
+| Ctrl+Shift+D | Diff view between two tabs |
+| F7 / Shift+F7 | Next / previous diff hunk |
+| Alt+Z | Toggle word wrap |
+| Ctrl+Plus / Minus / 0 | Zoom in / out / reset |
+| F1 | Help |
+
+> On macOS, use Cmd instead of Ctrl.
+
+---
+
+## Right-Click Context Menu
+
+Right-click any line in the log viewer for:
+
+- **Highlight "..."** — highlight the selected text across the file
+- **Include / Exclude "..."** — add selection to filter patterns
+- **Add Bookmark** / **Bookmark as "..."** — bookmark with optional label
+- **Range from here / Range to here** — select a line range for export or review
+- **Search from Ln N** — start searching from a specific line
+- **Copy Line** / **Copy Selection**
+
+---
+
+## Search Features
+
+Click the search options row to reveal:
+
+- **Regex** — full regular expression support
+- **Wildcard** — glob patterns (`*`, `?`)
+- **Match Case** / **Whole Word**
+- **Start Line** — search from a specific line number
+- **Column Config** — analyze CSV/TSV structure, toggle individual column visibility, search within specific columns
+
+LOGAN auto-detects if `ripgrep` (rg) is installed and uses it for 10-100x faster search. A badge in the status bar shows which engine is active.
+
+---
+
+## Filter System
+
+The filter bar supports combining multiple criteria:
+
+- **Include patterns** — lines must match at least one (OR)
+- **Exclude patterns** — lines matching any are hidden
+- **Level filter** — show only specific log levels
+- **Time range** — filter by timestamp window
+- **Context lines** — keep N surrounding lines around matches
+
+### Advanced Filter
+Build complex queries with groups of rules (`contains`, `not_contains`, `regex`, `level`) joined by AND/OR operators.
+
+### Hidden Match Peek
+When a filter is active and search results exist in hidden lines, a peek icon appears. Click it to see those hidden matches with surrounding context.
+
+---
+
+## Analysis & Baselines
+
+### Run Analysis (Ctrl+6)
+Detects crashes, errors, top failing components, and suggests filters. Click a suggestion to apply it instantly.
+
+### Baselines
+Save an analysis snapshot as a named baseline. Later, compare a different log against it to see:
+- **Level shifts** — error/warning percentages changed significantly
+- **New crashes** — crash keywords not present in baseline
+- **Component changes** — new or missing components
+- **Error rate spikes** — component error rate increased 2x or more
+- **Time pattern variance** — log density changed drastically
+
+---
+
+## Split & Diff View
+
+- **Split view** — open two files side by side with synchronized scrolling
+- **Diff view** (Ctrl+Shift+D) — compare current tab against the next tab, with added/removed lines color-coded
+- **F7 / Shift+F7** — jump between diff hunks
+- **Ctrl+PageDown / PageUp** — cycle through split files
+
+---
+
+## Live Connections (Ctrl+Shift+P)
+
+Connect to up to 4 live log sources simultaneously:
+
+### Serial
+Select a USB serial port and baud rate. Incoming data is captured to a temp file and displayed live.
+
+### Logcat (Android)
+Select an ADB device, optionally set a filter pattern. Captures `adb logcat` output.
+
+### SSH
+Create or load an SSH profile, specify a remote file path to tail. Supports key-based auth with passphrase prompts. Also provides SFTP browsing to download remote files.
+
+Each connection shows a card with a minimap preview, line count, duration, and stop/restart/save/remove controls.
+
+---
+
+## Notes Drawer (Ctrl+Shift+N)
+
+A slide-up text editor for freeform notes. Auto-saves to `.logan/<filename>.notes.txt` next to the log file.
+
+Use **Ctrl+Shift+S** (or right-click > Save Snippet) to append selected lines to the notes file.
+
+---
+
+## Terminal (Ctrl+\`)
+
+A Quake-style drop-down terminal from the top of the window. Full shell access (bash/zsh) without leaving LOGAN. Resizable by dragging the bottom edge.
+
+---
+
+## Bookmark Sets & Highlight Groups
+
+### Bookmark Sets
+Save all current bookmarks as a named set. Load a set later to restore bookmarks — useful for switching between investigation contexts on the same file.
+
+### Highlight Groups
+Save all current highlights as a named group. Load groups to quickly apply a color scheme for a specific log format or investigation.
+
+Both are stored globally in `~/.logan/` and available across files.
+
+---
+
+## Search Configs & Sessions
+
+Save frequently-used search patterns with colors as **search configs**. Group related configs into **sessions** and batch-run them against any file. Results show colored ranges on the minimap.
+
+---
+
+## Video Sync (Ctrl+9)
+
+Drag a video file into the Video Sync panel. Set a sync point linking a log line number to a video timestamp. As you scroll the log, the video seeks to the corresponding time — useful for correlating screen recordings with log output.
+
+---
+
+## Datadog Integration
+
+Fetch logs directly from Datadog into LOGAN:
+1. Enter your API key and App key
+2. Select your Datadog site (US1, US3, EU, or custom)
+3. Write a query and choose a time range
+4. Fetched logs open automatically in a new tab
+
+---
+
+## Column Filtering
+
+For structured logs (CSV, TSV, or fixed-width):
+1. Click **Analyze Columns** in the search options
+2. LOGAN auto-detects the delimiter and column structure
+3. Toggle individual columns on/off
+4. Search and display only the columns you care about
+
+---
+
+## Minimap
+
+The vertical bar on the right edge shows a visual overview of the entire file:
+- **Red** = errors, **Yellow** = warnings
+- **Colored marks** = highlights, search matches, bookmarks
+- **Click** to jump, **drag** to scroll
+- Live connection cards show a horizontal density minimap per connection
+
+---
+
+## Data Storage
+
+| Location | Contents |
+|----------|----------|
+| `.logan/<file>.json` | Bookmarks, file-specific highlights, history (next to log file) |
+| `.logan/<file>.notes.txt` | Notes for that file |
+| `~/.logan/highlights.json` | Global highlights |
+| `~/.logan/highlight-groups.json` | Saved highlight groups |
+| `~/.logan/bookmark-sets.json` | Saved bookmark sets |
+| `~/.logan/baselines.db` | Baseline snapshots (SQLite) |
+| `~/.logan/redaction-rules.json` | Custom redaction rules for MCP/AI |
+
+If the directory next to the log file is read-only, LOGAN falls back to `~/.logan/` with a keyed approach.
+
+---
+
+## MCP Server (AI Integration)
+
+LOGAN exposes an MCP server for AI agents (like Claude Code) to control it programmatically:
+
+```bash
+npm run mcp
+```
+
+The AI can open files, search, filter, analyze, manage bookmarks/highlights, save/compare baselines, and navigate — all through natural language. The server communicates via stdio (MCP protocol) to LOGAN's HTTP API on localhost.
+
+Sensitive data (IPs, emails, tokens) is automatically redacted before being sent to the AI. Custom redaction rules can be added in `~/.logan/redaction-rules.json`.