docs: update changelog, audit log, features, and readme for v0.5.6 code quality cleanup and keybinds customization

Author: VariableThe

AUDIT_LOG.md

@@ -2,6 +2,22 @@
 
 This log tracks all significant changes, updates, and versions in the PaperCache project.
 
+## 2026-06-29 (Code Quality Cleanup)
+**Change:** refactor: code quality cleanup — dead code, boilerplate, types, constants, AI comments; fix: address PR review findings — listener leak, type contracts, dead ref, stale guard, cfg scope, shortcut loop, timer constant
+
+**Details/Why:**
+1. **Dead Code Removal**: Removed `resumeTimer` no-op stub from useTimerStore; removed `onSwipeGesture` (ignored callback) from api.ts and types; removed `themePreset`/`setThemePreset` from useAppStore (duplicated in useSettingsStore, all consumers used the latter); removed `prevNotesRef` from useReminders (assigned but never read).
+2. **Boilerplate Consolidation**: `useAppStore.ts` — consolidated 9 setters into `booleanSetter`/`simpleSetter` helpers; `api.ts` — extracted 5×8-line identical listener patterns into shared `onEvent` helper; `KeybindsModal.tsx` — replaced 9 parallel `useState`/`getShortcut` calls with data-driven config array; `useSettingsStore.ts` — removed 11 redundant individual setters (use `setSettings` instead).
+3. **Rust Fixes**: Fixed clippy `needless_borrows_for_generic_args` in `notifications.rs`; added doc-commented `[lints.rust] unexpected_cfgs = "allow"` for objc crate macro warnings.
+4. **Type Safety**: `any` → typed `GraphControls` interface in GraphView; `Promise<unknown>` → properly typed `openAIChat` response; replaced unsafe `as` casts with wrapper functions; `pauseShortcuts`/`resumeShortcuts` changed to return `Promise<void>`.
+5. **Magic Numbers → Named Constants**: Extracted ~25 magic numbers across the codebase (z-indices, timeouts, force params, debounce intervals, canvas dimensions, etc.).
+6. **Comment Cleanup**: Removed ~15 pedagogical/AI-generated comments.
+7. **PR Review Fixes**: Fixed `onEvent` listener leak (added `disposed` flag); fixed stale-token guard in `useReminders` to gate before backend call; fixed `openAIChat` response validation for missing content; removed dead `searchInputRef`/`useEffect` in App.tsx; narrowed `unexpected_cfgs` suppression; made KeybindsModal global shortcut loop data-driven via config; aligned initial timer tick constant in TimersPage.
+
+**Files changed:** `src/store/useTimerStore.ts`, `src/api.ts`, `src/types.d.ts`, `src/setupTests.ts`, `src/store/useAppStore.ts`, `src/store/useAppStore.test.ts`, `src/store/useSettingsStore.ts`, `src/hooks/useReminders.ts`, `src/components/KeybindsModal.tsx`, `src/components/TimersPage.tsx`, `src/GraphView.tsx`, `src/App.tsx`, `src/lib/editor/extensions.ts`, `src/lib/editor/MathEvaluator.ts`, `src/lib/editor/VariableScope.ts`, `src/components/Editor.tsx`, `src-tauri/src/commands/notifications.rs`, `src-tauri/Cargo.toml`, `src-tauri/src/lib.rs`, `src-tauri/src/macos.rs`, `CHANGELOG.md`, `AUDIT_LOG.md`.
+
+---
+
 ## 2026-06-28 (v0.5.6 Release: Keybinds Modal, Shortcut Mappings, Timer Auto-Delete, and Graph Link Refinement)
 **Change:** chore(release): bump version to 0.5.6; feat(shortcuts): add dedicated keybinds settings modal and update global hotkeys (`Cmd+R` for tasks, `Cmd+T` for timers); feat(timers): auto-delete expired timers after 5 seconds; feat(graph): support standard markdown links and wikilinks
 

CHANGELOG.md

@@ -14,6 +14,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Updated Default Shortcut Mappings**: Shifted the Reminders/Tasks view shortcut to `Cmd+R` and Timers panel shortcut to `Cmd+T`.
 - **Timer Auto-Deletion**: Expired countdown timers are now automatically removed from the active list 5 seconds after completing, keeping the UI clean. Timer completion notifications and auto-cleanup now function globally even when the Timers panel is closed.
 - **Enhanced Graph View Link Parsing**: Extended 3D Graph View link detection to support standard markdown links (`[Note](Note.md)`) and wikilinks (`[[Note]]`) alongside the existing `/file` syntax, and added z-axis forces for improved 3D layout stability.
+- **Code Quality Cleanup**: Consolidated repetitive boilerplate across stores, event listeners, and UI components; extracted ~25 magic numbers into named constants; removed dead code and pedagogical AI-style comments.
+- **Improved Type Safety**: Replaced `any` with typed interfaces in GraphView; properly typed `openAIChat` API response; aligned async method return types across bridge API.
+- **Rust Lint Cleanup**: Fixed clippy warnings in notifications.rs; documented suppressions for legacy objc crate macro warnings.
 
 ## [v0.5.5] - 2026-06-27
 

README.md

@@ -75,14 +75,17 @@ Built with Tauri, Rust, React, TypeScript, and Vite.
 
 ## Shortcuts
 
+All shortcuts are fully customizable via Settings → Keybinds (`Cmd+Shift+S`). Defaults:
+
 | Shortcut      | Action                                   |
 | ------------- | ---------------------------------------- |
 | `Cmd+Shift+C` | Toggle visibility (global, configurable) |
 | `Cmd+Shift+N` | New note (global, configurable)          |
-| `Cmd+Shift+S` | Open settings panel                      |
+| `Cmd+Shift+S` | Open keybinds settings modal             |
 | `Cmd+N`       | New note (in-app)                        |
 | `Cmd+/`       | Open shortcuts reference                 |
-| `Cmd+T`       | Open Tasks page                          |
+| `Cmd+R`       | Open Tasks & Reminders page              |
+| `Cmd+T`       | Open Timers page                         |
 | `Cmd+K`       | Main action menu                         |
 | `Cmd+P`       | Search notes                             |
 | `Cmd+G`       | Graph view                               |

features.md

@@ -11,7 +11,7 @@ This document outlines every feature available in the PaperCache codebase, organ
 - **Date & Time Formats**: Highlights standard date (`DD-MM-YYYY` or `YYYY-MM-DD`) and time (`HH:MM` or `HH:MM:SS`) formats into clean, distinct pills.
 - **Slash Command Autosuggest**: Type `/` to trigger an inline ghost-text autosuggest for commands like `/check`, `/task`, `/ai`, or `/ctx`. Press `Tab` to instantly complete the command without breaking your typing flow.
 - **Interactive Checkboxes**: Type `/check` to create an interactive checkbox widget. Clicking it changes it to `/checked` and visually strikes through the text on that line!
-- **Tasks & Reminders**: Type `/task` to create a task widget. Add a space followed by `@` and a time (like `1d2h`, `tmrw`, or a specific date `YYYY-MM-DD HH:MM`) to set a due date. Press `Cmd+T` (or `Ctrl+T`) to open the Tasks Page, which tracks all tasks, calculates due times, and highlights overdue tasks in red.
+- **Tasks & Reminders**: Type `/task` to create a task widget. Add a space followed by `@` and a time (like `1d2h`, `tmrw`, or a specific date `YYYY-MM-DD HH:MM`) to set a due date. Press `Cmd+T` (or `Ctrl+T`) to open the Tasks Page, which tracks all tasks, calculates due times, and highlights overdue tasks in red. Expired timers are automatically removed from the list after 5 seconds to keep the UI clean.
 - **Customizable Theming & Fonts**: Customize fonts, text colors, background colors, background images, and individual highlight colors for variables, AI, and math. Supports full dark mode (`grid-dark`, `blueprint`).
 
 ## Math, Variables, and Calculations
@@ -28,6 +28,7 @@ This document outlines every feature available in the PaperCache codebase, organ
 - **Interactive Graph View** (`Cmd+G`): An interactive 2D knowledge graph rendered with Three.js WebGL. Nodes are clean flat circles with always-visible labels, edges are colored by opacity. Features:
   - **Folder Clustering**: Notes in the same folder are gently attracted toward a shared centroid, creating subtle visual groupings.
   - **Cmd+F Fuzzy Search**: Press `Cmd+F` inside graph view to fuzzy-search note names. Navigate with arrow keys, press Enter to fly the camera directly to the matched node.
+  - **Multi-Format Link Detection**: Automatically detects connections via standard markdown links (`[Note](Note.md)`), wikilinks (`[[Note]]`), and `/file Note` syntax.
   - **Drag to Rearrange**: Nodes can be dragged freely; positions are cached and restored across graph sessions.
   - **Smooth Fade-in**: The graph overlay animates in with a 250ms fade.
   - **Lazy-Loaded**: The Three.js bundle (~1.3 MB) loads only when the graph is first opened, keeping startup fast.
@@ -49,7 +50,7 @@ This document outlines every feature available in the PaperCache codebase, organ
 - **Stealth / Background Mode**: Click away or lose focus, and the app instantly hides itself (macOS) or after a brief debounce (Windows/Linux — prevents accidental hide when dragging the title bar). On macOS, it runs as an "accessory" and hides its dock icon completely, acting like a true floating utility.
 - **Intelligent Multi-Monitor Support**: When summoning the app via its global hotkey, it detects the active screen your mouse is currently on and brings the window instantly to that specific screen's workspace.
 - **System Tray Icon**: A minimal system tray icon for toggling visibility or quitting the app cleanly, adapting to the user's OS theme (light/dark).
-- **Global Hotkeys**:
+- **Global Hotkeys**: All shortcuts are fully customizable via Settings → Keybinds (`Cmd+Shift+S`). The keybinds modal lets you remap every action with live recording. Defaults include:
   - `Cmd+Shift+N` (configurable): Spawn a new note from anywhere. If the app is already open, creates the note without hiding.
   - `Cmd+Shift+C` (configurable): Toggle PaperCache visibility from anywhere on your OS.
 - **State Memory**: Memorizes precise window coordinates, dimensions, and zoom levels across launches to persist workspace state.