Update keyboard shortcuts documentation and formatting

shortcuts.md

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+# Keyboard Shortcuts
+
+This page lists the keyboard shortcuts available in Atom Architect.
+
+[1. General](#1-general)\
+[2. View](#2-view)\
+[3. Selection](#3-selection)\
+[4. Geometry Editing](#4-geometry-editing)\
+[5. NEB Analysis](#5-neb-analysis)
+
+> [!NOTE]
+> Most shortcuts are scoped to the active panel. Move the mouse over the **Editor** or **Geometry optimization** viewer to make that panel active before using panel-specific shortcuts.
+
+> [!IMPORTANT]
+> `Ctrl+Q` and `Ctrl+W` close the full program, regardless of which panel is active.
+
+## 1. General
+
+| Shortcut | Action | Where |
+| --- | --- | --- |
+| `Ctrl+O` | Open a file | Active Editor, Geometry optimization, or NEB window |
+| `Ctrl+S` | Save the current geometry | Editor |
+| `F2` | Show the debug log | Anywhere in the main program |
+
+## 2. View
+
+> [!NOTE]
+> These shortcuts work in the **Editor**, **Geometry optimization** viewer, and **NEB** viewer where available.
+
+### Camera Alignment
+
+| Shortcut | View |
+| --- | --- |
+| `0` | Default |
+| `7` | Top |
+| `Ctrl+7` | Bottom |
+| `3` | Left |
+| `Ctrl+3` | Right |
+| `1` | Front |
+| `Ctrl+1` | Back |
+
+### Camera Mode
+
+| Shortcut | Action |
+| --- | --- |
+| `5` | Perspective mode |
+| `Ctrl+5` | Orthographic mode |
+| `Ctrl+0` | Reset view |
+
+## 3. Selection
+
+> [!NOTE]
+> Selection shortcuts work in the **Editor**.
+
+Atoms are selected with the right mouse button (`RMB`). The first `RMB` press places atoms in the primary selection buffer. Pressing `RMB` again moves them into the secondary selection buffer.
+
+| Shortcut | Action |
+| --- | --- |
+| `Ctrl+A` | Select all atoms |
+| `Ctrl+D` | Deselect all atoms |
+| `Ctrl+I` | Invert selection |
+
+## 4. Geometry Editing
+
+> [!NOTE]
+> Geometry editing shortcuts work in the **Editor** viewport.
+
+### Manipulation
+
+| Shortcut | Action |
+| --- | --- |
+| `G` | Grab or move atoms in the primary selection buffer |
+| `R` | Rotate atoms in the primary selection buffer |
+| `Delete` | Delete atoms in the primary selection buffer |
+| `Shift+A` | Add the selected fragment to the system |
+
+When adding a fragment with `Shift+A`, the primary selection buffer sets the insertion position and the secondary selection buffer is used to construct the direction vector.
+
+After pressing `G`, use one of these follow-up keys to constrain movement:
+
+| Follow-up | Movement constraint |
+| --- | --- |
+| `X` | Move along the Cartesian X direction |
+| `Y` | Move along the Cartesian Y direction |
+| `Z` | Move along the Cartesian Z direction |
+| `F` | Move relative to the focal point defined by the secondary selection buffer |
+
+After pressing `R`, use one of these follow-up keys to choose the rotation mode:
+
+| Follow-up | Rotation mode |
+| --- | --- |
+| `X` | Rotate around an axis parallel to the Cartesian X direction |
+| `Y` | Rotate around an axis parallel to the Cartesian Y direction |
+| `Z` | Rotate around an axis parallel to the Cartesian Z direction |
+| `F` | Rotate around the focal point defined by the secondary selection buffer |
+| `S` | Revolve around the secondary selection buffer |
+| `C` | Revolve around the camera direction |
+
+### Constraints
+
+| Shortcut | Action |
+| --- | --- |
+| `Ctrl+F` | Freeze atoms in the primary selection buffer |
+| `Ctrl+Shift+F` | Unfreeze atoms in the primary selection buffer |
+
+### History
+
+| Shortcut | Action |
+| --- | --- |
+| `Ctrl+Z` | Undo the previous geometry edit |
+| `Ctrl+Y` | Redo the next geometry edit |
+
+## 5. NEB Analysis
+
+> [!NOTE]
+> These shortcuts are available in the separate **NEB** analysis window.
+
+| Shortcut | Action |
+| --- | --- |
+| `Left` | Show previous NEB image |
+| `Right` | Show next NEB image |
+| `Ctrl+O` | Open a NEB file |
+
+The NEB window also supports the camera alignment shortcuts listed in the **View** section.