feat: add align-repeat utility function for text alignment

Add comprehensive guide for agents working in this Doom Emacs config:
- Build/lint/test commands (doom sync, doom build, doom doctor)
- Emacs Lisp code style guidelines
- Doom macro reference (use-package!, add-hook!, map!, after!, load!)
- Naming conventions and common patterns
- Important workflow notes

.gitignore

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+# Emacs temporary files
+*~
+\#*\#
+.#*
+*.elc
+
+# Doom/Package generated
+auto-save-list/
+tramp/
+keyfreq.html
+
+# AI Assistant folders
+.claude/
+.opencode/
+
+# MacOS (just in case)
+.DS_Store
+
+
+
+

AGENTS.md

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+# AGENTS.md — Doom Emacs Configuration
+
+This is a Doom Emacs 3 personal configuration at `~/.config/doom/`.
+
+## Repository Structure
+
+```
+doom/
+├── init.el           # Module declarations (doom! macro)
+├── config.el         # Main config, loads modular files via load!
+├── packages.el       # Package declarations (package! macro)
+├── core.el           # Core settings and super-save
+├── custom.el         # Emacs custom variables (auto-generated)
+├── security.el       # Security settings
+├── org.el            # Org-mode configuration
+├── metrics.el        # Usage tracking (keyfreq)
+├── theme.el          # Theme configuration
+├── inbox.el          # Quick capture inbox
+├── ai/
+│   ├── agents.el     # Claude Code & Gemini CLI configuration
+│   └── gptel.el      # GPTel (ChatGPT) configuration
+├── development/
+│   ├── lsp.el        # LSP/LSP-UI configuration
+│   ├── cpp.el        # C++ development settings
+│   ├── nix.el        # Nix development settings
+│   └── misc.el       # Miscellaneous dev settings
+├── docs/
+│   └── doom-macros-reference.md  # Doom macro documentation
+└── snippets/         # Yasnippet snippets
+```
+
+## Doom Commands
+
+### Essential Commands
+
+```bash
+# Sync config (run after ANY change to init.el, packages.el, or package configs)
+doom sync
+
+# Rebuild all packages
+doom build
+
+# Diagnose issues
+doom doctor
+
+# Update all packages
+doom sync -u
+
+# Show verbose output
+doom -v sync
+
+# Run in batch mode (for CI/testing)
+emacs --batch -l ~/.config/doom/config.el --eval "(message \"test\")"
+```
+
+### Package Management
+
+```bash
+# Force sync without prompts
+doom sync -!
+
+# Clean up orphaned packages
+doom sync --gc
+
+# Install packages only (no rebuild)
+doom install
+```
+
+### Testing Individual Config Files
+
+```bash
+# Load a specific config file and check for errors
+emacs --batch -l ~/.config/emacs/bin/doom -l config.el -l ai/agents.el --eval "(message \"Loaded successfully\")"
+
+# Check Elisp syntax
+emacs --batch --eval "(setq lexical-binding t)" -l ai/agents.el --eval "(message \"Syntax OK\")"
+```
+
+## Code Style Guidelines (Emacs Lisp)
+
+### File Headers
+
+Every `.el` file should start with a standard header:
+
+```elisp
+;;; filename.el -*- lexical-binding: t; -*-
+
+;;; Commentary:
+;;; Description of what this file does
+
+;;; Code:
+```
+
+### Lexical Binding
+
+Always use `lexical-binding: t` (note the dash, not underscore in the file-local variable).
+
+```elisp
+;;; init.el -*- lexical-binding: t; -*-
+```
+
+### Naming Conventions
+
+| Element | Convention | Example |
+|---------|------------|---------|
+| Private functions | `+prefix--name` | `+org--restart-mode-h` |
+| Hook functions | `+module-hook-function-h` | `+org-exclude-agenda-buffers-from-workspace-h` |
+| Variables | `+module-variable-name` | `+org--restart-mode-h` |
+| Package hooks | `-module-hook-function-h` | `-org-exclude-agenda-buffers-from-workspace-h` |
+| Doom modules | `:module` | `:lang`, `:completion` |
+| Module flags | `+flag` | `+orderless`, `+lsp` |
+| Constants | `SCREAMING-SNAKE` | `MAX-HEIGHT` |
+
+### Keybinding Syntax (map!)
+
+```elisp
+;; Basic keybindings
+(map! :n "C-s" #'consult-line)
+
+;; With lambda
+(map! :n "M-s" (lambda () (interactive) (consult-line (thing-at-point 'symbol))))
+
+;; Leader key with prefix
+(map! :leader
+      (:prefix ("C" . "claude-code")
+       :desc "Start Claude" "c" #'claude-code
+       :desc "Kill Claude" "k" #'claude-code-kill))
+
+;; State modifiers: :n (normal), :v (visual), :i (insert), :e (emacs)
+(map! :nv "C-j" #'something)
+```
+
+### use-package! vs use-package
+
+- Use `use-package!` in Doom configs (macro version)
+- Use `use-package` when referring to the built-in package.el macro
+
+```elisp
+;; Doom configuration
+(use-package! org-roam
+  :after org
+  :custom
+  (org-roam-directory "~/org/roam")
+  :config
+  (org-roam-db-autosync-mode))
+
+;; Standard Emacs (when needed)
+(use-package org
+  :init
+  (setq org-todo-keywords '("TODO" "DONE"))
+  :config
+  (org-mode 1))
+```
+
+### Hook Registration
+
+```elisp
+;; Anonymous function with defun inside
+(add-hook! 'org-agenda-finalize-hook
+  (defun +org-exclude-agenda-buffers-from-workspace-h ()
+    "Don't associate temporary agenda buffers with current workspace."
+    (when org-agenda-new-buffers
+      (persp-remove-buffer org-agenda-new-buffers
+                           (get-current-persp)
+                           nil))))
+
+;; :local makes hook buffer-local
+(add-hook! :local 'some-mode-hook
+  (defun my-local-hook ()
+    (do-something)))
+```
+
+### Conditional Loading
+
+```elisp
+;; After package loads (preferred in Doom)
+(after! lsp-ui
+  (setq lsp-ui-doc-enable t))
+
+;; With feature check
+(when (featurep! :system 'macos)
+  (setq mac-command-modifier 'meta))
+
+;; After multiple packages
+(after! (org org-roam)
+  (require 'org-roam-protocol))
+```
+
+### Defcustom vs Defvar
+
+- Use `defcustom` for user-configurable settings that belong in `custom.el`
+- Use `defvar` or `setq` for internal variables
+
+```elisp
+;; In packages.el (for user customization)
+(setq org-directory "~/org/")
+
+;; Not a defcustom unless it belongs in custom.el
+```
+
+### Error Handling
+
+```elisp
+;; Use quiet! to suppress output
+(quiet! (org-mode-restart))
+
+;; Use fn! or #' for function references
+(advice-add #'org-capture :around
+            (lambda (fun &rest args)
+              (letf! ((#'+org--restart-mode-h #'ignore))
+                (apply fun args))))
+
+;; Use ignore when function should do nothing
+(defalias '+org--restart-mode-h #'ignore)
+```
+
+### Package Recipes (packages.el)
+
+```elisp
+;; Simple package from Melpa
+(package! super-save)
+
+;; GitHub recipe with custom files
+(package! copilot
+  :recipe (:host github :repo "copilot-emacs/copilot.el" :files ("*.el")))
+
+;; GitHub with exclusion patterns
+(package! eat
+  :recipe (:host codeberg
+           :repo "akib/emacs-eat"
+           :files ("*.el" ("term" "term/*.el") "*.texi"
+                   "*.ti" ("terminfo/e" "terminfo/e/*")
+                   (:exclude ".dir-locals.el" "*-tests.el"))))
+
+;; Disable a package
+(package! some-package :disable t)
+```
+
+## Common Patterns
+
+### Restart/Reload Functions
+
+```elisp
+(defun +org--restart-mode-h ()
+  "Restart org-mode on buffer switch."
+  (remove-hook 'doom-switch-buffer-hook #'+org--restart-mode-h 'local)
+  (cl-delete (current-buffer) org-agenda-new-buffers :test 'eq)
+  (quiet! (org-mode-restart))
+  (run-hooks 'find-file-hook))
+```
+
+### Advice Around Functions
+
+```elisp
+(advice-add #'org-capture :around
+            (lambda (fun &rest args)
+              (letf! ((#'+org--restart-mode-h #'ignore))
+                (apply fun args))))
+```
+
+### Buffer Display Configuration
+
+```elisp
+(add-to-list 'display-buffer-alist
+             '("^\\*claude"
+               (display-buffer-in-side-window)
+               (side . right)
+               (window-width . 90)))
+```
+
+### Environment Variables
+
+```elisp
+;; Unset for subprocess access
+(setenv "CLAUDECODE" nil)
+
+;; Set with path
+(setenv "PATH" (concat "/usr/local/bin:" (getenv "PATH")))
+```
+
+## Doom Module System
+
+The `init.el` uses the `doom!` macro to declare enabled modules:
+
+```elisp
+(doom! :category
+       (module +flag)
+       :another-category)
+```
+
+Modules referenced in this config:
+- `:completion` — Vertico, Corfu
+- `:ui` — Doom dashboard, treemacs, workspaces
+- `:editor` — Evil, format+, multiple-cursors
+- `:emacs` — Dired, ibuffer, undo
+- `:term` — Eshell, vterm
+- `:checkers` — Syntax, spell
+- `:tools` — LSP, magit, direnv, docker
+- `:lang` — Python, Go, Rust, Org, JavaScript, etc.
+- `:config` — Default bindings, smartparens
+
+## Important Notes
+
+1. Run `doom sync` after ANY change to `init.el`, `packages.el`, or `config.el`
+2. Use `doom build` to rebuild if byte-compilation errors occur
+3. This config uses straight.el for package management (via Doom)
+4. Custom variables are auto-generated to `custom.el` — don't edit manually
+5. The `load!` macro loads relative to `doom-private-dir` (this config directory)

ai/agents.el

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+;;; ai/agents.el -*- lexical-binding: t; -*-
+
+;;; ============================================================================
+;;; Claude Code Configuration
+;;; ============================================================================
+
+(use-package! claude-code
+  :defer t
+  :config
+  ;; Unset CLAUDECODE to allow running Claude Code inside Emacs sub-processes
+  (setenv "CLAUDECODE" nil)
+  (setq claude-code-program "ccr"
+        claude-code-program-switches '("code" "--dangerously-skip-permissions"))
+
+  ;; Use Eat backend
+  (setq claude-code-terminal-backend 'eat
+        ;; Emacs-style editing in Claude buffer: RET inserts newline, S-RET sends
+        claude-code-newline-keybinding-style 'shift-return-to-send)
+
+  ;; Enable global mode
+  (claude-code-mode 1)
+
+  ;; Emacs-style prefix key (works without Doom/Evil leader keys)
+  (global-set-key (kbd "C-c c") claude-code-command-map)
+
+  ;; Set Doom leader keybindings
+  (map! :leader
+        (:prefix ("C" . "claude-code")
+         :desc "Start Claude" "c" #'claude-code
+         :desc "Start in directory" "d" #'claude-code-start-in-directory
+         :desc "Continue conversation" "C" #'claude-code-continue
+         :desc "Resume session" "R" #'claude-code-resume
+         :desc "New instance" "i" #'claude-code-new-instance
+         :desc "Kill Claude" "k" #'claude-code-kill
+         :desc "Kill all instances" "K" #'claude-code-kill-all
+         :desc "Send command" "s" #'claude-code-send-command
+         :desc "Send command with context" "x" #'claude-code-send-command-with-context
+         :desc "Send region/buffer" "r" #'claude-code-send-region
+         :desc "Send buffer file" "o" #'claude-code-send-buffer-file
+         :desc "Fix error at point" "e" #'claude-code-fix-error-at-point
+         :desc "Toggle window" "t" #'claude-code-toggle
+         :desc "Switch to buffer" "b" #'claude-code-switch-to-buffer
+         :desc "Select buffer" "B" #'claude-code-select-buffer
+         :desc "Toggle read-only" "z" #'claude-code-toggle-read-only-mode
+         :desc "Cycle mode" "M" #'claude-code-cycle-mode
+         :desc "Transient menu" "m" #'claude-code-transient
+         :desc "Slash commands" "/" #'claude-code-slash-commands
+         :desc "Fork conversation" "f" #'claude-code-fork
+         :desc "Send return" "y" #'claude-code-send-return
+         :desc "Send escape" "n" #'claude-code-send-escape
+         :desc "Send 1" "1" #'claude-code-send-1
+         :desc "Send 2" "2" #'claude-code-send-2
+         :desc "Send 3" "3" #'claude-code-send-3))
+
+  ;; Optional: Configure window display (side window on right)
+  (add-to-list 'display-buffer-alist
+               '("^\\*claude"
+                 (display-buffer-in-side-window)
+                 (side . right)
+                 (window-width . 90)))
+
+  ;; Optional: Enable auto-revert for files modified by Claude
+  (global-auto-revert-mode 1)
+
+  ;; Optional: Increase vterm scrollback for long conversations
+  (add-hook 'claude-code-start-hook
+            (lambda ()
+              (when (eq claude-code-terminal-backend 'vterm)
+                (setq-local vterm-max-scrollback 100000)))))
+
+;;; ============================================================================
+;;; Gemini CLI Configuration
+;;; ============================================================================
+
+(use-package! gemini-cli
+  :defer t
+  :config
+  ;; Set the Gemini executable
+  (setq gemini-cli-program "gemini"
+        gemini-cli-program-switches nil)
+
+  ;; Use Eat backend
+  (setq gemini-cli-terminal-backend 'eat
+        ;; Emacs-style editing in Gemini buffer: RET inserts newline, S-RET sends
+        gemini-cli-newline-keybinding-style 'shift-return-to-send)
+
+  ;; Enable global mode
+  (gemini-cli-mode 1)
+
+  ;; Emacs-style prefix key
+  (global-set-key (kbd "C-c g") gemini-cli-command-map)
+
+  ;; Set Doom leader keybindings under SPC G
+  (map! :leader
+        (:prefix ("G" . "gemini-cli")
+         :desc "Start Gemini" "c" #'gemini-cli
+         :desc "Start in directory" "d" #'gemini-cli-start-in-directory
+         :desc "Continue conversation" "C" #'gemini-cli-continue
+         :desc "Resume session" "R" #'gemini-cli-resume
+         :desc "New instance" "i" #'gemini-cli-new-instance
+         :desc "Kill Gemini" "k" #'gemini-cli-kill
+         :desc "Kill all instances" "K" #'gemini-cli-kill-all
+         :desc "Send command" "s" #'gemini-cli-send-command
+         :desc "Send command with context" "x" #'gemini-cli-send-command-with-context
+         :desc "Send region/buffer" "r" #'gemini-cli-send-region
+         :desc "Send buffer file" "o" #'gemini-cli-send-buffer-file
+         :desc "Fix error at point" "e" #'gemini-cli-fix-error-at-point
+         :desc "Toggle window" "t" #'gemini-cli-toggle
+         :desc "Switch to buffer" "b" #'gemini-cli-switch-to-buffer
+         :desc "Select buffer" "B" #'gemini-cli-select-buffer
+         :desc "Toggle read-only" "z" #'gemini-cli-toggle-read-only-mode
+         :desc "Cycle mode" "M" #'gemini-cli-cycle-mode
+         :desc "Transient menu" "m" #'gemini-cli-transient
+         :desc "Slash commands" "/" #'gemini-cli-slash-commands
+         :desc "Fork conversation" "f" #'gemini-cli-fork
+         :desc "Send return" "y" #'gemini-cli-send-return
+         :desc "Send escape" "n" #'gemini-cli-send-escape
+         :desc "Send 1" "1" #'gemini-cli-send-1
+         :desc "Send 2" "2" #'gemini-cli-send-2
+         :desc "Send 3" "3" #'gemini-cli-send-3))
+
+  ;; Optional: Configure window display (side window on right)
+  (add-to-list 'display-buffer-alist
+               '("^\\*gemini"
+                 (display-buffer-in-side-window)
+                 (side . right)
+                 (window-width . 90)))
+
+  ;; Optional: Increase vterm scrollback for long conversations
+  (add-hook 'gemini-cli-start-hook
+            (lambda ()
+              (when (eq gemini-cli-terminal-backend 'vterm)
+                (setq-local vterm-max-scrollback 100000)))))

ai/gptel.el

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+;;; ai/gptel.el -*- lexical-binding: t; -*-
+
+;;; ============================================================================
+;;; gptel Configuration
+;;; ============================================================================
+
+;; Core gptel setup
+(use-package! gptel
+  :defer t
+  :config
+  ;; Default backend: OpenRouter
+  (setq gptel-model 'google/gemini-3-flash-preview
+        gptel-backend
+        (gptel-make-openai "OpenRouter"
+          :host "openrouter.ai"
+          :endpoint "/api/v1/chat/completions"
+          :stream t
+          :key "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"
+          :models '(google/gemini-3-flash-preview
+                    x-ai/grok-4.1-fast
+                    x-ai/grok-code-fast-1
+                    google/gemini-3-pro-preview
+                    anthropic/claude-sonnet-4.5)))
+
+  ;; Use org-mode by default for better note-taking
+  (setq gptel-default-mode 'org-mode)
+
+  ;; Move cursor to end of response automatically
+  (add-hook 'gptel-post-response-functions 'gptel-end-of-response)
+
+  ;; Keybindings - using SPC A for AI (uppercase to avoid conflicts)
+  (map! :leader
+        (:prefix ("A" . "AI/gptel")
+         :desc "gptel chat" "g" #'gptel
+         :desc "gptel send" "s" #'gptel-send
+         :desc "gptel menu" "m" #'gptel-menu
+         :desc "gptel rewrite" "r" #'gptel-rewrite
+         :desc "Add context" "c" #'gptel-add
+         :desc "Add file to context" "f" #'gptel-add-file))
+
+  ;; Additional keybindings in gptel buffer
+  (map! :map gptel-mode-map
+        "C-c RET" #'gptel-send
+        "C-c C-k" #'gptel-abort
+        "C-c C-c" #'gptel-menu))
+
+;; gptel presets for different tasks
+(after! gptel
+  ;; Coding assistant preset
+  (gptel-make-preset 'coder
+    :description "Expert coding assistant"
+    :backend "OpenRouter"
+    :model 'anthropic/claude-sonnet-4.5
+    :system "You are an expert coding assistant. Provide high-quality code solutions, refactorings, and explanations. Be concise but thorough. Include error handling and follow best practices.")
+
+  ;; Code explainer preset
+  (gptel-make-preset 'explain
+    :description "Explain code to beginners"
+    :system "Explain this code to a novice programmer. Use simple language and break down complex concepts.")
+
+  ;; Refactoring preset
+  (gptel-make-preset 'refactor
+    :description "Code refactoring expert"
+    :model 'anthropic/claude-sonnet-4.5
+    :system "You are a code refactoring expert. Improve code quality, readability, and performance while maintaining functionality. Explain your changes.")
+
+  ;; Quick answers preset
+  (gptel-make-preset 'quick
+    :description "Quick, concise answers"
+    :model 'google/gemini-3-flash-preview
+    :system "Provide quick, concise answers. Be direct and to the point.")
+
+  ;; Documentation writer preset
+  (gptel-make-preset 'docs
+    :description "Documentation writer"
+    :system "Write clear, comprehensive documentation. Include examples and explain edge cases."))
+
+;;; ============================================================================
+;;; gptel-quick - Quick lookups and explanations
+;;; ============================================================================
+
+(use-package! gptel-quick
+  :after gptel
+  :defer t
+  :config
+  ;; Include context from gptel-add if available
+  (setq gptel-quick-use-context t)
+
+  (map! :leader
+        (:prefix "A"
+         :desc "Quick lookup" "q" #'gptel-quick)))
+
+;;; ============================================================================
+;;; gptel-extensions - Extra utility functions
+;;; ============================================================================
+
+(use-package! gptel-extensions
+  :after gptel
+  :defer t
+  :config
+  (map! :leader
+        (:prefix "A"
+         :desc "Load buffer into session" "l" #'gptel-extensions-load-buffer
+         :desc "Send whole buffer" "b" #'gptel-extensions-send-whole-buffer
+         :desc "Refactor region" "R" #'gptel-extensions-refactor)))
+
+;;; ============================================================================
+;;; gptel-autocomplete - Inline code completion
+;;; ============================================================================
+
+(use-package! gptel-autocomplete
+  :after gptel
+  :defer t
+  :commands (gptel-complete gptel-accept-completion)
+  :config
+  ;; Configure context size
+  (setq gptel-autocomplete-before-context-lines 100
+        gptel-autocomplete-after-context-lines 20
+        gptel-autocomplete-temperature 0.1)
+
+  ;; Keybindings for autocomplete
+  (map! :leader
+        (:prefix "A"
+         :desc "Complete at point" "C" #'gptel-complete
+         :desc "Accept completion" "a" #'gptel-accept-completion))
+
+  ;; Also add convenient keybindings in prog-mode
+  (map! :map prog-mode-map
+        "M-TAB" #'gptel-complete
+        "C-c TAB" #'gptel-complete
+        "C-c C-a" #'gptel-accept-completion))
+
+(defun my/gptel-quick-explain-region ()
+  "Quickly explain selected code region in the gptel buffer."
+  (interactive)
+  (when (use-region-p)
+    (let* ((code (buffer-substring-no-properties (region-beginning) (region-end)))
+           (buf (get-buffer-create "*gptel*")))
+      ;; Prepare the buffer and insert the query immediately
+      (with-current-buffer buf
+        (goto-char (point-max))
+        (unless (derived-mode-p 'gptel-mode)
+          (funcall gptel-default-mode)
+          (gptel-mode 1))
+        (insert "\n\n--- Code to Explain ---\n\n" code "\n\n### Explanation Request Sent...\n"))
+      (display-buffer buf)
+      ;; Send the request
+      (gptel-request
+          (format "Explain this code concisely in 2-3 sentences:\n\n%s" code)
+        :system "You are an expert programmer explaining code."
+        :callback (lambda (response info)
+                    (with-current-buffer (get-buffer "*gptel*")
+                      (goto-char (point-max))
+                      (insert "\n### Code Explanation\n\n" response "\n\n"))
+                    (message "Explanation received in *gptel* buffer."))))))
+
+(defun my/gptel-proofread-region ()
+  "Proofread and improve selected text."
+  (interactive)
+  (when (use-region-p)
+    (gptel-rewrite-region (region-beginning) (region-end)
+                          "Fix spelling, grammar, and improve clarity. Keep the same tone and style.")))
+
+(defun my--get-region-as-path-tag (path-fn)
+  "Helper to get path tag using PATH-FN to determine the file path."
+  (let* ((filename (funcall path-fn))
+         (start-line (line-number-at-pos (if (use-region-p) (region-beginning) (point))))
+         (tag (if (use-region-p)
+                  (let* ((end-pos (1- (region-end)))
+                         (end-line (line-number-at-pos (max (region-beginning) end-pos))))
+                    (format "@%s:%d-%d" filename start-line end-line))
+                (format "@%s:%d" filename start-line))))
+    tag))
+
+(defun my/copy-region-as-path-tag ()
+  "Copy the current region as a relative path tag: @path/to/file.ext:start-end"
+  (interactive)
+  (let ((tag (my--get-region-as-path-tag
+              (lambda () (file-relative-name (buffer-file-name) (doom-project-root))))))
+    (kill-new tag)
+    (message "Copied: %s" tag)))
+
+(defun my/copy-region-as-path-tag-absolute ()
+  "Copy the current region as an absolute path tag: @/abs/path/to/file.ext:start-end"
+  (interactive)
+  (let ((tag (my--get-region-as-path-tag #'buffer-file-name)))
+    (kill-new tag)
+    (message "Copied: %s" tag)))
+
+;; Add keybindings for helper functions
+(defvar my-ai-helper-map (make-sparse-keymap)
+  "Keymap for my AI helper functions.")
+
+(global-set-key (kbd "C-c a") my-ai-helper-map)
+(define-key my-ai-helper-map (kbd "e") #'my/gptel-quick-explain-region)
+(define-key my-ai-helper-map (kbd "p") #'my/gptel-proofread-region)
+(define-key my-ai-helper-map (kbd "t") #'my/copy-region-as-path-tag)
+(define-key my-ai-helper-map (kbd "T") #'my/copy-region-as-path-tag-absolute)
+
+(map! :leader
+      (:prefix "A"
+       :desc "Quick explain" "e" #'my/gptel-quick-explain-region
+       :desc "Proofread text" "p" #'my/gptel-proofread-region
+       :desc "Copy path tag (relative)" "t" #'my/copy-region-as-path-tag
+       :desc "Copy path tag (absolute)" "T" #'my/copy-region-as-path-tag-absolute))

config.el

@@ -1,320 +1,23 @@
 ;;; $DOOMDIR/config.el -*- lexical-binding: t; -*-
 
-(setq doom-theme 'doom-one)
+;; Load modular configuration files
+(load! "security")
+(load! "core")
+(load! "development/lsp")
+(load! "development/cpp")
+(load! "development/nix")
+(load! "development/misc")
+(load! "org")
+(load! "ai/gptel")
+(load! "ai/agents")
+(load! "inbox")
+(load! "metrics")
+(load! "theme")
 
-(setq display-line-numbers-type t)
+;; Performance tweaks
+(setq gc-cons-threshold 100000000  ; Increase GC threshold to 100MB
+      gc-cons-percentage 0.6)
+(run-with-idle-timer 5 t #'garbage-collect)
 
-(setq org-directory "~/org/")
-
-(defun load-if-exists (f)
-  (if (file-exists-p (expand-file-name f))
-      (load-file (expand-file-name f))))
-
-(load-if-exists "~/.config/doom/secrets.el")
-
-(after! epa-file
-  (setq epa-file-encrypt-to "[email protected]"))
-
-(after! auth-source
-  (setq auth-sources '("~/.authinfo.gpg")))
-
-(setq epa-file-cache-passphrase-for-symmetric-encryption t)
-
-(use-package! super-save
-  :config
-  (super-save-mode +1)
-  (setq super-save-auto-save-when-idle t)
-  (setq super-save-idle-duration 1))
-
-
-;; Search bindings for consult-line
-(map!
- :n "C-s" (lambda () (interactive) (consult-line (thing-at-point 'symbol)))
- :n "M-S" #'consult-line
- :n "C-S-s" #'consult-line-multi)
-
-(after! lsp-ui
-  (setq lsp-ui-doc-include-signature t     ;; Show method signatures in docs
-        lsp-ui-sideline-show-symbol t      ;; Show symbols in the sideline
-        lsp-ui-doc-show-with-cursor t      ;; Show docs when cursor is on symbol
-        lsp-ui-doc-max-height 30           ;; Increase doc height to show more info
-        lsp-ui-sideline-show-hover t       ;; Show hover information in sideline
-        lsp-ui-doc-enable t                ;; Enable documentation
-        lsp-signature-auto-activate t       ;; Show signature help automatically
-        lsp-signature-render-documentation t)) ;; Include docs in signature help
-
-(after! eldoc
-  (setq eldoc-echo-area-use-multiline-p t
-        eldoc-echo-area-prefer-doc-buffer t))
-
-(use-package! corfu-popupinfo
-  :after corfu
-  :hook (corfu-mode . corfu-popupinfo-mode)
-  :custom
-  (corfu-popupinfo-delay '(0.25 . 0.1)) ; Faster popup display
-  (corfu-popupinfo-hide nil)            ; Don't hide automatically
-  ) 
-
-;; Configure Corfu for richer display
-(after! corfu
-  (setq corfu-auto t                      ; Enable auto completion
-        corfu-auto-prefix 2               ; Complete after 2 characters
-        corfu-preview-current t           ; Preview current candidate
-        corfu-show-documentation t        ; Show documentation in popup
-        corfu-doc-max-height 20           ; Max height for doc popup
-        corfu-doc-delay 0.2               ; Faster doc popup
-        corfu-quit-no-match t)             ; Quit if no match
-
-  ;; Show more detailed annotations
-  (setq corfu-show-annotations t
-        corfu-annotate-max-width 50))
-
-;; If using LSP, configure to show more details
-(after! lsp-mode
-  (setq lsp-completion-show-detail t           ; Show method signatures
-        lsp-completion-show-kind t             ; Show completion item kind
-        lsp-completion-show-label-description t ; Show more details in label
-        ))
-
-(after! lsp-haskell
-  (setq lsp-haskell-plugin-fourmolu-config-path "fourmolu -o -XImportQualifiedPost -o -XOverloadedStrings -o -XTypeApplications -o -XScopedTypeVariables -o -XGADTs -o -XDataKinds -o -XTypeFamilies -o -XFlexibleContexts -o -XFlexibleInstances -o -XMultiParamTypeClasses -o -XRankNTypes -o -XExistentialQuantification")
-  )
-
-
-(defun +org--restart-mode-h ()
-  "Restart `org-mode', but only once."
-  (remove-hook 'doom-switch-buffer-hook #'+org--restart-mode-h
-               'local)
-  (delq! (current-buffer) org-agenda-new-buffers)
-  (let ((file buffer-file-name)
-        (old-buffer (current-buffer))
-        (inhibit-redisplay t)
-        new-buffer)
-    (kill-buffer)
-    (setq new-buffer (find-file file))
-    (unless (buffer-live-p old-buffer)
-      (make-indirect-buffer new-buffer old-buffer 'clone))))
-
-(defun +org--restart-mode-h ()
-  "Restart `org-mode', but only once."
-  (remove-hook 'doom-switch-buffer-hook #'+org--restart-mode-h
-               'local)
-  (delq! (current-buffer) org-agenda-new-buffers)
-  (let ((file buffer-file-name)
-        (inhibit-redisplay t))
-    (kill-buffer)
-    (find-file file)))
-(defun +org--restart-mode-h ()
-  "Restart `org-mode', but only once."
-  (remove-hook 'doom-switch-buffer-hook #'+org--restart-mode-h 'local)
-  (quiet! (org-mode-restart))
-  (delq! (current-buffer) org-agenda-new-buffers)
-  (run-hooks 'find-file-hook))
-
-(add-hook! 'org-agenda-finalize-hook
-  (defun +org-exclude-agenda-buffers-from-workspace-h ()
-    "Don't associate temporary agenda buffers with current workspace."
-    (when (and org-agenda-new-buffers
-               (bound-and-true-p persp-mode)
-               (not org-agenda-sticky))
-      (let (persp-autokill-buffer-on-remove)
-        (persp-remove-buffer org-agenda-new-buffers
-                             (get-current-persp)
-                             nil)))))
-
-
-(use-package org
-  :defer t
-  :config
-  (defalias '+org--restart-mode-h #'ignore))
-
-(advice-add #'org-capture :around
-            (lambda (fun &rest args)
-              (letf! ((#'+org--restart-mode-h #'ignore))
-                (apply fun args))))
-
-;;(use-package! org-roam
-;;   :after org
-;;   :config
-;;   :init
-;;   (setq org-roam-directory "~/org/roam")  ; No file-truename needed in Doom
-;;   :config
-;;   (advice-remove 'org-roam-db-query '+org-roam-try-init-db-a)
-;;   (org-roam-db-autosync-mode)
-;;   (setq org-roam-completion-everywhere t))
-
-                                        ; (use-package! org-roam
-                                        ;   :custom
-                                        ;   (org-roam-directory "~/org/roam")
-                                        ;   (org-roam-completion-everywhere t)
-                                        ;   (org-roam-capture-templates
-                                        ;    '(("d" "default" plain
-                                        ;       "%?"
-                                        ;       :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
-                                        ;                          "#+title: ${title}\n")
-                                        ;       :unnarrowed t)
-                                        ;      ("r" "reference" plain
-                                        ;       "%?"
-                                        ;       :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
-                                        ;                          "#+title: ${title}\n#+filetags: :reference:\n")
-                                        ;       :unnarrowed t)
-                                        ;      ("p" "project" plain
-                                        ;       "\n* Goals\n\n%?\n\n* Tasks\n\n* Notes\n\n"
-                                        ;       :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
-                                        ;                          "#+title: ${title}\n#+filetags: :project:\n")
-                                        ;       :unnarrowed t)))
-                                        ;   :config
-                                        ;   (org-roam-setup)
-                                        ;   ;; If using org-roam-protocol
-                                        ;   (require 'org-roam-protocol))
-
-(after! org
-  (require 'org-re-reveal)
-  (setq org-re-reveal-root "https://cdn.jsdelivr.net/npm/reveal.js")
-  (setq org-re-reveal-theme "white")
-  (setq org-re-reveal-transition "slide"))
-
-(after! org
-  (require 'org-tempo)
-  (add-to-list 'org-structure-template-alist '("n" . "notes")))
-
-(use-package! anki-editor
-  :after org
-  :config
-  (setq anki-editor-create-decks t)
-  :bind (:map org-mode-map
-              ("C-c a" . anki-editor-push-notes)))
-
-(use-package! org-anki
-  :after org
-  :config
-  (setq org-anki-default-deck "Default")
-  :bind (:map org-mode-map
-              ("C-c n" . org-anki-sync-entry)))
-
-(setq-default show-trailing-whitespace t)
-
-(use-package! bnf-mode
-  :mode "\\.bnf\\'"
-  :config
-  ;; Optional: Add any custom configuration here
-  (setq bnf-mode-hook
-        (lambda ()
-          ;; Enable line numbers
-          (display-line-numbers-mode)
-          ;; Enable auto-pairing of angle brackets
-          (modify-syntax-entry ?< "(>" bnf-mode-syntax-table)
-          (modify-syntax-entry ?> ")<" bnf-mode-syntax-table))))
-
-(use-package! ebnf-mode
-  :mode "\\.ebnf\\'"
-  :config
-  ;; Optional customizations:
-  (setq ebnf-mode-indent-offset 4)        ; Default is 8 spaces
-  (setq ebnf-mode-indent-by-production t) ; Align with the '=' in productions
-  (setq ebnf-mode-comment-char ?\;)       ; Use ; for comments
-  (setq ebnf-mode-eop-char ?\.))         ; Use . for end of production
-
-(use-package! nix-mode
-  :mode "\\.nix\\'"
-  :config
-  ;; Function to check if we're in a nixpkgs repository
-  (defun in-nixpkgs-repo-p ()
-    (when-let ((root (or (locate-dominating-file default-directory ".git")
-                         (vc-root-dir))))
-      (or (string-match-p "/nixpkgs/?$" root)
-          (file-exists-p (expand-file-name "pkgs/top-level/all-packages.nix" root))
-          (file-exists-p (expand-file-name ".nixpkgs-version.json" root)))))
-
-  ;; Set up format-all-mode to use our custom formatter selection
-  (set-formatter! 'nixfmt
-    '("nixfmt")
-    :modes '(nix-mode))
-
-  (set-formatter! 'alejandra
-    '("alejandra" "--quiet")
-    :modes '(nix-mode))
-
-  ;; Add hooks to handle all formatting scenarios
-  (add-hook! 'nix-mode-hook
-             ;; Disable LSP formatting
-             (setq-local +format-with-lsp nil)
-
-             ;; Set formatter for format-all-mode (+format/buffer)
-             (setq-local +format-with
-                         (if (in-nixpkgs-repo-p)
-                             'nixfmt
-                           'alejandra))
-
-             ;; Handle format-on-save
-             (when (bound-and-true-p format-all-mode)
-               (format-all-mode -1))
-             (add-hook! 'before-save-hook :local
-               (when (eq major-mode 'nix-mode)
-                 (if (in-nixpkgs-repo-p)
-                     (format-all-buffer 'nixfmt)
-                   (format-all-buffer 'alejandra))))
-
-             ;; Override lsp-format-buffer
-             (advice-add 'lsp-format-buffer :around
-                         (lambda (orig-fun &rest args)
-                           (if (eq major-mode 'nix-mode)
-                               (if (in-nixpkgs-repo-p)
-                                   (format-all-buffer 'nixfmt)
-                                 (format-all-buffer 'alejandra))
-                             (apply orig-fun args))))))
-
-;; Enable format-on-save globally if desired
-(setq +format-on-save-enabled-modes '(nix-mode))
-
-(use-package! llvm-ts-mode
-  :mode "\\.ll\\'"          ; LLVM IR files
-  :mode "\\.td\\'"          ; TableGen files
-  :hook (llvm-ts-mode . tree-sitter-mode))
-
-(after! tree-sitter
-  (add-to-list 'tree-sitter-major-mode-language-alist '(llvm-ts-mode . llvm)))
-
-(after! lsp-clangd
-  (setq lsp-clients-clangd-executable "clangd")
-  (setq lsp-clients--clangd-default-executable "clangd")
-  (setq lsp-clangd-binary-path "clangd"))
-
-(after! org
-  (use-package! ob-mermaid
-    :config
-    (setq ob-mermaid-cli-path "mmdc"))  ; Adjust path if needed
-
-  ;; Add mermaid to org-babel languages
-  (org-babel-do-load-languages
-   'org-babel-load-languages
-   (append org-babel-load-languages
-           '((mermaid . t)))))
-
-(after! org
-  (setq-default org-download-image-dir "./images")
-
-  (defun my/org-download-image-dir-setup ()
-    "Create and set org-download-image-dir relative to current org file."
-    (let* ((current-file-dir (file-name-directory (buffer-file-name)))
-           (image-dir (expand-file-name "images" current-file-dir)))
-      (make-directory image-dir t)
-      (setq-local org-download-image-dir image-dir)))
-
-  (add-hook 'org-mode-hook #'my/org-download-image-dir-setup)
-  (setq org-download-link-format "[[file:%s]]\n")
-  (setq org-download-timestamp "%Y%m%d-%H%M%S_")
-  (setq org-download-screenshot-method "maim -s %s")
-  )
-
-(setq gptel-model   'mixtral-8x7b-32768
-      gptel-backend
-      (gptel-make-openai "OpenRouter"               ;Any name you want
-        :host "openrouter.ai"
-        :endpoint "/api/v1/chat/completions"
-        :stream t
-        :key "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"                   ;can be a function that returns the key
-        :models '(google/gemini-2.5-flash-preview-05-20
-                  google/gemini-2.5-flash-preview-05-20:thinking
-                  anthropic/claude-sonnet-4
-                  )))
+;; Keybinding to open inbox.el
+(map! "C-c i" #'(lambda () (interactive) (find-file (expand-file-name "inbox.el" doom-user-dir))))

core.el

@@ -0,0 +1,25 @@
+;;; core.el -*- lexical-binding: t; -*-
+
+(setq doom-theme 'doom-one)
+
+(setq display-line-numbers-type t)
+
+(setq org-directory "~/org/")
+
+(use-package! super-save
+  :config
+  (super-save-mode +1)
+  (setq super-save-auto-save-when-idle t)
+  (setq super-save-idle-duration 1))
+
+;; Which-key: show keybindings faster
+(setq which-key-idle-delay 0.01
+      which-key-min-display-time 0.1)
+
+;; Search bindings for consult-line
+(map!
+ :n "C-s" #'consult-line
+ :n "M-s" (lambda () (interactive) (consult-line (thing-at-point 'symbol)))
+ :n "C-S-s" #'consult-line-multi)
+
+(setq-default show-trailing-whitespace nil)

custom.el

@@ -0,0 +1,15 @@
+;;; -*- lexical-binding: t -*-
+(custom-set-variables
+ ;; custom-set-variables was added by Custom.
+ ;; If you edit it by hand, you could mess it up, so be careful.
+ ;; Your init file should contain only one such instance.
+ ;; If there is more than one, they won't work right.
+ '(custom-safe-themes
+   '("0325a6b5eea7e5febae709dab35ec8648908af12cf2d2b569bedc8da0a3a81c1"
+     "8a379e7ac3a57e64de672dd744d4730b3bdb88ae328e8106f95cd81cbd44e0b6" default)))
+(custom-set-faces
+ ;; custom-set-faces was added by Custom.
+ ;; If you edit it by hand, you could mess it up, so be careful.
+ ;; Your init file should contain only one such instance.
+ ;; If there is more than one, they won't work right.
+ )

development/cpp.el

@@ -0,0 +1,43 @@
+;;; development/cpp.el -*- lexical-binding: t; -*-
+
+;; 4. Optional: Fine-tuning Clangd
+;; These arguments are passed directly to the clangd binary.
+(setq lsp-clients-clangd-args
+      '("-j=4"
+        "--background-index"
+        "--clang-tidy"
+        "--completion-style=detailed"
+        "--header-insertion=never"
+        "--header-insertion-decorators=0"))
+
+(after! lsp-clangd
+  (set-lsp-priority! 'clangd 2)) ; Ensure clangd is preferred over ccls
+
+;; Formatting for c++
+;; This tells Doom to use the LSP server (clangd) for formatting instead of
+;; a separate clang-format call via apheleia.
+(setq-hook! '(c-mode-hook c++-mode-hook) +format-with-lsp t)
+
+;; Formatting as I type
+;; This enables real-time formatting as you type trigger characters like ; or }
+(after! lsp-mode
+  (setq lsp-enable-on-type-formatting t))
+
+;; Ensure cc-mode settings align with clangd/clang-format
+;; While clangd handles most things, basic Emacs indentation settings are
+;; still useful as a fallback or for initial indentation.
+(after! cc-mode
+  (setq-default c-basic-offset 2)
+  (c-add-style "doom-cpp"
+               '("llvm"
+                 (c-basic-offset . 2)
+                 (c-offsets-alist . ((innamespace . 0)
+                                     (access-label . -)
+                                     (arglist-intro . +)
+                                     (arglist-cont-nonempty . +)))))
+  (add-hook! '(c-mode-hook c++-mode-hook)
+    (c-set-style "doom-cpp")))
+
+;; Add C++ documentation support
+(set-docsets! 'c++-mode "C++")
+(set-docsets! 'c-mode "C")

development/lsp.el

@@ -0,0 +1,44 @@
+;;; development/lsp.el -*- lexical-binding: t; -*-
+
+(after! lsp-ui
+  (setq lsp-ui-doc-include-signature t     ;; Show method signatures in docs
+        lsp-ui-sideline-show-symbol t      ;; Show symbols in the sideline
+        lsp-ui-doc-show-with-cursor t      ;; Show docs when cursor is on symbol
+        lsp-ui-doc-max-height 30           ;; Increase doc height to show more info
+        lsp-ui-sideline-show-hover t       ;; Show hover information in sideline
+        lsp-ui-doc-enable t                ;; Enable documentation
+        lsp-signature-auto-activate t       ;; Show signature help automatically
+        lsp-signature-render-documentation t)) ;; Include docs in signature help
+
+(after! eldoc
+  (setq eldoc-echo-area-use-multiline-p t
+        eldoc-echo-area-prefer-doc-buffer t))
+
+(use-package! corfu-popupinfo
+  :after corfu
+  :hook (corfu-mode . corfu-popupinfo-mode)
+  :custom
+  (corfu-popupinfo-delay '(0.25 . 0.1)) ; Faster popup display
+  (corfu-popupinfo-hide nil)            ; Don't hide automatically
+  )
+
+;; Configure Corfu for richer display
+(after! corfu
+  (setq corfu-auto t                      ; Enable auto completion
+        corfu-auto-prefix 2               ; Complete after 2 characters
+        corfu-preview-current t           ; Preview current candidate
+        corfu-show-documentation t        ; Show documentation in popup
+        corfu-doc-max-height 20           ; Max height for doc popup
+        corfu-doc-delay 0.2               ; Faster doc popup
+        corfu-quit-no-match t)             ; Quit if no match
+
+  ;; Show more detailed annotations
+  (setq corfu-show-annotations t
+        corfu-annotate-max-width 50)
+  )
+
+(after! lsp-mode
+  (setq lsp-completion-show-detail t           ; Show method signatures
+        lsp-completion-show-kind t             ; Show completion item kind
+        lsp-completion-show-label-description t ; Show more details in label
+        ))

development/misc.el

@@ -0,0 +1,39 @@
+;;; development/misc.el -*- lexical-binding: t; -*-
+
+(use-package! bnf-mode
+  :mode "\\.bnf\\'"
+  :config
+  ;; Optional: Add any custom configuration here
+  (setq bnf-mode-hook
+        (lambda ()
+          ;; Enable line numbers
+          (display-line-numbers-mode)
+          ;; Enable auto-pairing of angle brackets
+          (modify-syntax-entry ?< "(>" bnf-mode-syntax-table)
+          (modify-syntax-entry ?> ")<" bnf-mode-syntax-table))))
+
+(use-package! ebnf-mode
+  :mode "\\.ebnf\\'"
+  :config
+  ;; Optional customizations:
+  (setq ebnf-mode-indent-offset 4)        ; Default is 8 spaces
+  (setq ebnf-mode-indent-by-production t) ; Align with the '=' in productions
+  (setq ebnf-mode-comment-char ?\;)       ; Use ; for comments
+  (setq ebnf-mode-eop-char ?\.))         ; Use . for end of production
+
+;; Devicetree mode (ZMK keymap, .dts, .dtsi)
+(use-package! dts-mode
+  :mode ("\\.keymap\\'" "\\.dts\\'" "\\.dtsi\\'"))
+
+;; Justfile mode (psibi/justl.el)
+(use-package! justl
+  :config
+  (map! :n "e" 'justl-exec-recipe))
+
+;; align-repeat: repeatedly align region by a given regexp/character
+;; From EmacsWiki: https://www.emacswiki.org/emacs/AlignCommands
+(defun align-repeat (start end regexp)
+  "Repeat alignment with respect to the given regular expression."
+  (interactive "r\nsAlign regexp: ")
+  (align-regexp start end
+                (concat "\\(\\s-*\\)" regexp) 1 1 t))

development/nix.el

@@ -0,0 +1,73 @@
+;;; development/nix.el -*- lexical-binding: t; -*-
+
+(use-package! nix-mode
+  :mode "\\.nix\\'"
+  :hook (nix-mode . lsp-deferred)
+  :config
+  ;; Configure nil LSP server
+  (after! lsp-mode
+    (add-to-list 'lsp-language-id-configuration '(nix-mode . "nix"))
+    (lsp-register-client
+     (make-lsp-client :new-connection (lsp-stdio-connection "nil")
+                      :major-modes '(nix-mode)
+                      :server-id 'nil-ls
+                      :priority 0)))
+
+  ;; Function to check if we're in a nixpkgs repository
+  (defun in-nixpkgs-repo-p ()
+    (when-let ((root (or (locate-dominating-file default-directory ".git")
+                         (vc-root-dir))))
+      (or (string-match-p "/nixpkgs/?$" root)
+          (file-exists-p (expand-file-name "pkgs/top-level/all-packages.nix" root))
+          (file-exists-p (expand-file-name ".nixpkgs-version.json" root)))))
+
+  ;; Set up format-all-mode to use our custom formatter selection
+  (set-formatter! 'nixfmt
+    '("nixfmt")
+    :modes '(nix-mode))
+
+  (set-formatter! 'alejandra
+    '("alejandra" "--quiet")
+    :modes '(nix-mode))
+
+  ;; Add hooks to handle all formatting scenarios
+  (add-hook! 'nix-mode-hook
+             ;; Disable LSP formatting
+             (setq-local +format-with-lsp nil)
+
+             ;; Set formatter for format-all-mode (+format/buffer)
+             (setq-local +format-with
+                         (if (in-nixpkgs-repo-p)
+                             'nixfmt
+                           'alejandra))
+
+             ;; Handle format-on-save
+             (when (bound-and-true-p format-all-mode)
+               (format-all-mode -1))
+             (add-hook! 'before-save-hook :local
+               (when (eq major-mode 'nix-mode)
+                 (if (in-nixpkgs-repo-p)
+                     (format-all-buffer 'nixfmt)
+                   (format-all-buffer 'alejandra))))
+
+             ;; Override lsp-format-buffer
+             (advice-add 'lsp-format-buffer :around
+                         (lambda (orig-fun &rest args)
+                           (if (eq major-mode 'nix-mode)
+                               (let ((fmt (if (in-nixpkgs-repo-p)
+                                              (executable-find "nixfmt")
+                                            (executable-find "alejandra"))))
+                                 (when fmt
+                                   (format-all-buffer (intern (file-name-nondirectory fmt)))))
+                             (apply orig-fun args))))))
+
+;; Enable format-on-save globally if desired
+(setq +format-on-save-enabled-modes '(nix-mode))
+
+(use-package! llvm-ts-mode
+  :mode "\\.ll\\'"          ; LLVM IR files
+  :mode "\\.td\\'"          ; TableGen files
+  :hook (llvm-ts-mode . tree-sitter-mode))
+
+(after! tree-sitter
+  (add-to-list 'tree-sitter-major-mode-language-alist '(llvm-ts-mode . llvm)))

docs/doom-macros-reference.md

@@ -0,0 +1,283 @@
+# Doom Emacs Macros and Keywords Reference
+
+This document describes the macros and their keywords used in Doom Emacs 3 configuration.
+
+## Table of Contents
+
+- [`doom!` - Module Declaration](#doom---module-declaration)
+- [`package!` - Package Declaration](#package---package-declaration)
+- [`use-package!` / `use-package` - Package Configuration](#use-package--use-package---package-configuration)
+- [`add-hook!` - Hook Registration](#add-hook---hook-registration)
+- [`setq-hook!` - Set Variables in Hooks](#setq-hook---set-variables-in-hooks)
+- [`map!` - Keybinding](#map---keybinding)
+- [`after!` - Run Code After Package](#after---run-code-after-package)
+- [`load!` - Load Sub-config Files](#load---load-sub-config-files)
+
+---
+
+## `doom!` - Module Declaration
+
+Declares enabled modules and their flags in `init.el`.
+
+**Location:** `init.el`
+
+**Syntax:**
+```elisp
+(doom! :module
+       (module +flag1 +flag2)
+       :another-module)
+```
+
+**Keywords:** Module names and optional flags (prefixed with `+`).
+
+**Example:**
+```elisp
+(doom! :completion
+       (company +orderless)
+       :lang
+       (org +brain +crypt)
+       :tools
+       lsp)
+```
+
+---
+
+## `package!` - Package Declaration
+
+Declares packages to install in `packages.el`.
+
+**Location:** `packages.el`
+
+| Keyword | Description |
+|---------|-------------|
+| `:recipe` | MELPA-style straight recipe with `:host`, `:repo`, `:branch`, `:files`, etc. |
+| `:disable` | Disable the package (`t` to disable) |
+| `:built-in` | Mark as built-in (`'prefer`) |
+| `:pin` | Pin to a specific commit hash |
+| `:local-repo` | Local repository path |
+
+**Example:**
+```elisp
+(package! super-save)
+
+(package! copilot
+  :recipe (:host github :repo "copilot-emacs/copilot.el" :files ("*.el")))
+
+(package! org-re-reveal :disable t)
+```
+
+---
+
+## `use-package!` / `use-package` - Package Configuration
+
+Configures packages with a declarative DSL.
+
+**Location:** `config.el` or modular config files
+
+| Keyword | Description |
+|---------|-------------|
+| `:init` | Code to run immediately (before package loads) |
+| `:config` | Code to run after package loads |
+| `:defer` | Defer loading (boolean or integer seconds) |
+| `:after` | Load after another package or packages |
+| `:hook` | Hook into specific hooks |
+| `:bind` | Define key bindings |
+| `:commands` | Autoload commands |
+| `:custom` | Set customization variables |
+| `:custom-face` | Customize faces |
+| `:pre-init` | Run before package's own `:init` |
+| `:pre-config` | Run before package's own `:config` |
+| `:post-init` | Run after package's own `:init` |
+| `:post-config` | Run after package's own `:config` |
+
+**Example:**
+```elisp
+(use-package! org-roam
+  :after org
+  :custom
+  (org-roam-directory "~/org/roam")
+  (org-roam-completion-everywhere t)
+  :config
+  (org-roam-db-autosync-mode)
+  :bind (("C-c n l" . org-roam-buffer-toggle)
+         ("C-c n f" . org-roam-node-find)))
+```
+
+### Hook Syntax
+
+```elisp
+(use-package! some-package
+  :hook ((prog-mode . some-package-mode)
+         (org-mode . some-package-mode)))
+```
+
+### Bind Syntax with Maps
+
+```elisp
+(use-package! anki-editor
+  :after org
+  :bind (:map org-mode-map
+              ("C-c a" . anki-editor-push-notes)))
+```
+
+---
+
+## `add-hook!` - Hook Registration
+
+Add hooks with inline function definitions.
+
+**Location:** Any config file
+
+| Keyword | Description |
+|---------|-------------|
+| `:local` | Make the hook local to current buffer |
+
+**Syntax:**
+```elisp
+(add-hook! HOOK-SPEC
+  (defun my-hook-function ()
+    "Description."
+    (do-something)))
+```
+
+**Example:**
+```elisp
+(add-hook! 'org-agenda-finalize-hook
+  (defun +org-exclude-agenda-buffers-from-workspace-h ()
+    "Don't associate temporary agenda buffers with current workspace."
+    (when (and org-agenda-new-buffers
+               (bound-and-true-p persp-mode)
+               (not org-agenda-sticky))
+      (let (persp-autokill-buffer-on-remove)
+        (persp-remove-buffer org-agenda-new-buffers
+                             (get-current-persp)
+                             nil)))))
+```
+
+---
+
+## `setq-hook!` - Set Variables in Hooks
+
+Set variables specifically for particular mode hooks.
+
+**Syntax:**
+```elisp
+(setq-hook! MODE-SPEC VARS...)
+```
+
+**Example:**
+```elisp
+(setq-hook! 'python-mode-hook
+  python-indent-offset 4
+  python-shell-interpreter "bpython")
+```
+
+---
+
+## `map!` - Keybinding
+
+Define key bindings with a declarative syntax.
+
+**Location:** Any config file
+
+| Keyword | State/Scope |
+|---------|-------------|
+| `:leader` | Normal state leader key (SPC) |
+| `:n` | Normal state |
+| `:v` | Visual state |
+| `:i` | Insert state |
+| `:e` | Emacs state |
+| `:o` | Operator-pending state |
+| `:ic` | Insert+normal (after ESC) |
+| `:nv` | Normal+visual combined |
+| `:after` | Delay until package loads |
+| `:map` | Specific keymap |
+| `:prefix` | Key sequence prefix |
+| `:desc` | Description for which-key display |
+
+**Syntax:**
+```elisp
+(map! KEYCOMBO COMMAND
+      KEYCOMBO COMMAND
+      ...)
+
+(map! :leader
+      (:prefix ("KEY" . "DESC")
+       KEYCOMBO COMMAND
+       ...))
+```
+
+**Example:**
+```elisp
+(map! :n "C-s" #'consult-line
+      :n "M-s" (lambda () (interactive) (consult-line (thing-at-point 'symbol))))
+
+(map! :leader
+      (:prefix ("C" . "claude-code")
+       :desc "Start Claude" "c" #'claude-code
+       :desc "Kill Claude" "k" #'claude-code-kill))
+```
+
+---
+
+## `after!` - Run Code After Package
+
+Run code after a package loads (shorthand for `with-eval-after-load`).
+
+**Syntax:**
+```elisp
+(after! PACKAGE
+  BODY...)
+```
+
+**Example:**
+```elisp
+(after! org
+  (require 'org-re-reveal)
+  (setq org-re-reveal-root "https://cdn.jsdelivr.net/npm/reveal.js"))
+```
+
+---
+
+## `load!` - Load Sub-config Files
+
+Load additional configuration files from `config.el`.
+
+**Location:** `config.el`
+
+**Syntax:**
+```elisp
+(load! "path/to/file")  ; Without .el extension
+```
+
+**Example:**
+```elisp
+;; In config.el
+(load! "security")
+(load! "core")
+(load! "org")
+(load! "ai/gptel")
+```
+
+---
+
+## Summary Table
+
+| Macro | Purpose | Location |
+|-------|---------|----------|
+| `doom!` | Declare enabled modules | `init.el` |
+| `package!` | Declare packages to install | `packages.el` |
+| `use-package!` | Configure packages | `config.el` or modular configs |
+| `add-hook!` | Register hooks | Any config file |
+| `setq-hook!` | Set vars for mode hooks | Any config file |
+| `map!` | Define keybindings | Any config file |
+| `after!` | Run code after package loads | Any config file |
+| `load!` | Load sub-config files | `config.el` |
+
+---
+
+## See Also
+
+- [Doom Emacs Documentation](https://docs.doomemacs.org)
+- [Doom Modules Index](https://github.com/doomemacs/doomemacs/blob/master/docs/modules.org)
+- [Getting Started Guide](https://github.com/doomemacs/doomemacs/blob/master/docs/getting_started.org)

inbox.el

@@ -0,0 +1,37 @@
+;;; inbox.el -*- lexical-binding: t; -*-
+
+;; Use this file for new packages and configuration snippets
+;; before sorting them into their proper places.
+
+(defun df/copy-file-line-ref ()
+  "Copy absolute file path with line reference as @/path#Lline or @/path#Lstart-end."
+  (interactive)
+  (let* ((file (or (buffer-file-name) (buffer-name)))
+         (abs-file (if (file-name-absolute-p file) file (expand-file-name file)))
+         (ref
+          (if (use-region-p)
+              (let* ((start (region-beginning))
+                     (end (region-end))
+                     (start-line (line-number-at-pos start))
+                     (end-line (line-number-at-pos (max start (1- end)))))
+                (format "@%s#L%d-%d" abs-file start-line end-line))
+            (format "@%s#L%d" abs-file (line-number-at-pos (point))))))
+    (kill-new ref)
+    (when (fboundp 'gui-set-selection)
+      (gui-set-selection 'CLIPBOARD ref))
+    (message "%s" ref)))
+
+(global-set-key (kbd "M-S w") #'df/copy-file-line-ref)
+
+(defun load-current-file ()
+  (interactive)
+  (load (buffer-file-name)))
+
+(global-set-key (kbd "C-c l") #'load-current-file)
+
+(use-package! command-log-mode
+  :config
+  (map! "C-c L" #'(lambda () (interactive)
+                   (command-log-mode (if command-log-mode -1 +1))
+                   (when command-log-mode
+                     (switch-to-buffer "*Command Log*")))))

init.el

@@ -48,6 +48,7 @@
        ;;unicode           ; extended unicode support for various languages
        (vc-gutter +pretty) ; vcs diff in the fringe
        vi-tilde-fringe   ; fringe tildes to mark beyond EOB
+       (which-key +popup) ; key binding popups
        window-select     ; visually switch windows
        workspaces        ; tab emulation, persistence & separate workspaces
        zen               ; distraction-free coding or writing
@@ -78,7 +79,7 @@
        eshell            ; the elisp shell that works everywhere
        ;;shell             ; simple shell REPL for Emacs
        ;;term              ; basic terminal emulator for Emacs
-       ;;vterm             ; the best terminal emulation in Emacs
+       vterm             ; the best terminal emulation in Emacs
 
        :checkers
        syntax              ; tasing you for every semicolon you forget
@@ -114,7 +115,7 @@
        :lang
        ;;agda              ; types of types of types of types...
        ;;beancount         ; mind the GAAP
-       (cc +lsp)         ; C > C++ == 1
+       (cc +lsp +tree-sitter)         ; C > C++ == 1
        ;;clojure           ; java with a lisp
        ;;common-lisp       ; if you've seen one lisp, you've seen them all
        ;;coq               ; proofs-as-programs
@@ -150,7 +151,7 @@
        ;;lua               ; one-based indices? one-based indices
        markdown          ; writing docs for people to ignore
        ;;nim               ; python + lisp at the speed of c
-       nix               ; I hereby declare "nix geht mehr!"
+       (nix +lsp)        ; I hereby declare "nix geht mehr!"
        ;;ocaml             ; an objective camel
        (org +brain
             +contacts
@@ -159,7 +160,6 @@
             +gnuplot
             +hugo
             +journal
-            +jupyter
             +link
             +noter
             +pandoc

metrics.el

@@ -0,0 +1,33 @@
+;;; metrics.el -*- lexical-binding: t; -*-
+
+;;; Keyfreq - Track command usage statistics
+(use-package! keyfreq
+  :config
+  (keyfreq-mode 1)
+  (keyfreq-autosave-mode 1)
+  (setq keyfreq-file      (concat doom-cache-dir "keyfreq")
+        keyfreq-file-lock (concat doom-cache-dir "keyfreq.lock"))
+  
+  ;; Optional: Exclude commands you don't want to track (uncomment to use)
+  ;; (setq keyfreq-excluded-commands
+  ;;       '(self-insert-command
+  ;;         forward-char
+  ;;         backward-char
+  ;;         previous-line
+  ;;         next-line))
+  )
+
+;;; Command Log Mode - visual log of keystrokes and commands
+(use-package! command-log-mode
+  :config
+  ;; Global mode to track everywhere
+  ;; (global-command-log-mode 1) ; Uncomment if you want it always on (can be noisy)
+  
+  (map! :leader
+        (:prefix ("t" . "toggle")
+         :desc "Toggle command log" "L" #'clm/toggle-command-log-buffer))
+  )
+
+
+
+

org.el

@@ -0,0 +1,135 @@
+;;; org.el -*- lexical-binding: t; -*-
+
+(defun +org--restart-mode-h ()
+  "Restart org-mode on buffer switch."
+  (remove-hook 'doom-switch-buffer-hook #'+org--restart-mode-h 'local)
+  (cl-delete (current-buffer) org-agenda-new-buffers :test 'eq)
+  (quiet! (org-mode-restart))
+  (run-hooks 'find-file-hook))
+
+(add-hook! 'org-agenda-finalize-hook
+  (defun +org-exclude-agenda-buffers-from-workspace-h ()
+    "Don't associate temporary agenda buffers with current workspace."
+    (when (and org-agenda-new-buffers
+               (bound-and-true-p persp-mode)
+               (not org-agenda-sticky))
+      (let (persp-autokill-buffer-on-remove)
+        (persp-remove-buffer org-agenda-new-buffers
+                             (get-current-persp)
+                             nil)))))
+
+
+(use-package org
+  :defer t
+  :config
+  (defalias '+org--restart-mode-h #'ignore))
+
+(advice-add #'org-capture :around
+            (lambda (fun &rest args)
+              (letf! ((#'+org--restart-mode-h #'ignore))
+                (apply fun args))))
+
+(use-package! org-roam
+  :after org
+  :custom
+  (org-roam-directory "~/org/roam")
+  (org-roam-completion-everywhere t)
+  (org-roam-capture-templates
+   '(("d" "default" plain
+      "%?"
+      :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                         "#+title: ${title}\n")
+      :unnarrowed t)
+     ("r" "reference" plain
+      "%?"
+      :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                         "#+title: ${title}\n#+filetags: :reference:\n")
+      :unnarrowed t)
+     ("p" "project" plain
+      "\n* Goals\n\n%?\n\n* Tasks\n\n* Notes\n\n"
+      :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                         "#+title: ${title}\n#+filetags: :project:\n")
+      :unnarrowed t)))
+  :config
+  (org-roam-db-autosync-mode)
+  :bind (("C-c n l" . org-roam-buffer-toggle)
+         ("C-c n f" . org-roam-node-find)
+         ("C-c n r" . org-roam-node-random)))
+
+                                        ; (use-package! org-roam
+                                        ;   :custom
+                                        ;   (org-roam-directory "~/org/roam")
+                                        ;   (org-roam-completion-everywhere t)
+                                        ;   (org-roam-capture-templates
+                                        ;    '(("d" "default" plain
+                                        ;       "%?"
+                                        ;       :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                                        ;                          "#+title: ${title}\n")
+                                        ;       :unnarrowed t)
+                                        ;      ("r" "reference" plain
+                                        ;       "%?"
+                                        ;       :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                                        ;                          "#+title: ${title}\n#+filetags: :reference:\n")
+                                        ;       :unnarrowed t)
+                                        ;      ("p" "project" plain
+                                        ;       "\n* Goals\n\n%?\n\n* Tasks\n\n* Notes\n\n"
+                                        ;       :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                                        ;                          "#+title: ${title}\n#+filetags: :project:\n")
+                                        ;       :unnarrowed t)))
+                                        ;   :config
+                                        ;   (org-roam-setup)
+                                        ;   ;; If using org-roam-protocol
+                                        ;   (require 'org-roam-protocol))
+
+(after! org
+  (require 'org-re-reveal)
+  (setq org-re-reveal-root "https://cdn.jsdelivr.net/npm/reveal.js")
+  (setq org-re-reveal-theme "white")
+  (setq org-re-reveal-transition "slide"))
+
+(after! org
+  (require 'org-tempo)
+  (add-to-list 'org-structure-template-alist '("n" . "notes")))
+
+(use-package! anki-editor
+  :after org
+  :config
+  (setq anki-editor-create-decks t)
+  :bind (:map org-mode-map
+              ("C-c a" . anki-editor-push-notes)))
+
+(use-package! org-anki
+  :after org
+  :config
+  (setq org-anki-default-deck "Default")
+  :bind (:map org-mode-map
+              ("C-c n" . org-anki-sync-entry)))
+
+(after! org
+  (use-package! ob-mermaid
+    :config
+    (setq ob-mermaid-cli-path "mmdc"))  ; Adjust path if needed
+
+  ;; Add mermaid to org-babel languages
+  (org-babel-do-load-languages
+   'org-babel-load-languages
+   (append org-babel-load-languages
+           '((mermaid . t)))))
+
+(after! org
+  (setq-default org-download-image-dir "./images")
+
+  (defun my/org-download-image-dir-setup ()
+    "Create and set org-download-image-dir relative to current org file."
+    (let ((filename (buffer-file-name)))
+      (when filename
+        (let* ((current-file-dir (file-name-directory filename))
+               (image-dir (expand-file-name "images" current-file-dir)))
+          (make-directory image-dir t)
+          (setq-local org-download-image-dir image-dir)))))
+
+  (add-hook 'org-mode-hook #'my/org-download-image-dir-setup)
+  (setq org-download-link-format "[[file:%s]]\n")
+  (setq org-download-timestamp "%Y%m%d-%H%M%S_")
+  (setq org-download-screenshot-method "maim -s %s")
+  )

packages.el

@@ -1,10 +1,21 @@
-;; -*- no-byte-compile: t; -*-
 ;;; $DOOMDIR/packages.el
+;; -*- no-byte-compile: t; -*-
 
 (package! super-save)
 
+;; gptel and extensions
 (package! gptel)
 
+;; gptel extensions
+(package! gptel-quick
+  :recipe (:host github :repo "karthink/gptel-quick"))
+
+(package! gptel-extensions
+  :recipe (:host github :repo "kamushadenes/gptel-extensions.el"))
+
+(package! gptel-autocomplete
+  :recipe (:host github :repo "JDNdeveloper/gptel-autocomplete"))
+
 (package! org-re-reveal)
 
 (package! copilot
@@ -29,3 +40,45 @@
 (package! tree-sitter-langs)
 
 (package! ob-mermaid)
+
+;; Claude Code integration
+(package! inheritenv
+  :recipe (:host github :repo "purcell/inheritenv"))
+
+(package! consult)
+
+(package! popup)
+
+(package! claude-code
+  :recipe (:host github :repo "stevemolitor/claude-code.el" :branch "main" :depth 1
+           :files ("*.el" (:exclude "images/*"))))
+
+(package! gemini-cli
+  :recipe (:host github :repo "linchen2chris/gemini-cli.el" :branch "main"
+           :files ("*.el" (:exclude "demo.gif"))))
+
+(package! claudemacs
+  :recipe (:host github :repo "cpoile/claudemacs"))
+
+;; Terminal emulator
+(package! eat
+  :recipe (:host codeberg
+           :repo "akib/emacs-eat"
+           :files ("*.el" ("term" "term/*.el") "*.texi"
+                   "*.ti" ("terminfo/e" "terminfo/e/*")
+                   ("terminfo/65" "terminfo/65/*")
+                   ("integration" "integration/*")
+                   (:exclude ".dir-locals.el" "*-tests.el"))))
+
+;; Justfile mode
+(package! justl :recipe (:host github :repo "psibi/justl.el"))
+
+;; Usage metrics and key tracking
+(package! keyfreq)
+(package! command-log-mode)
+
+;; Theme
+(package! base16-theme)
+(package! ewal)
+(package! ewal-doom-themes
+  :recipe (:host github :repo "cyruseuros/ewal" :files ("doom-themes/*.el")))

security.el

@@ -0,0 +1,15 @@
+;;; security.el -*- lexical-binding: t; -*-
+
+(defun load-if-exists (f)
+  (if (file-exists-p (expand-file-name f))
+      (load-file (expand-file-name f))))
+
+(load-if-exists "~/.config/doom/secrets.el")
+
+(after! epa-file
+  (setq epa-file-encrypt-to "[email protected]"))
+
+(after! auth-source
+  (setq auth-sources '("~/.authinfo.gpg")))
+
+(setq epa-file-cache-passphrase-for-symmetric-encryption t)

snippets/org-mode/anki-basic

@@ -0,0 +1,14 @@
+# -*- mode: snippet -*-
+# name: Anki Basic (Subheadings)
+# key: <a
+# --
+* ${1:Title} :study_card:
+:PROPERTIES:
+:ANKI_NOTE_TYPE: Basic
+:END:
+
+** Front
+$2
+
+** Back
+$3

theme.el

@@ -0,0 +1,20 @@
+;;; theme.el -*- lexical-binding: t; -*-
+
+;; Default Doom Theme
+(setq doom-theme 'doom-one)
+
+;; --- Ewal Configuration ---
+(use-package! ewal
+  :disabled t
+  :init
+  (setq ewal-json-file "~/.cache/wal/colors.json"
+        ewal-use-built-in-always-p nil
+        ewal-use-built-in-on-failure-p t
+        ewal-built-in-palette "sexy-material"))
+
+(use-package! ewal-doom-themes
+  :disabled t
+  :config
+  (load-theme 'ewal-doom-one t)
+  (enable-theme 'ewal-doom-one)
+  )