feat(ai): add gemini-cli integration with doom leader bindings

Switch Claude Code usage toward EAT-related setup and simplify theme loading to doom-one while adding the emacs-eat package declaration.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.gitignore

@@ -0,0 +1,20 @@
+# Emacs temporary files
+*~
+\#*\#
+.#*
+*.elc
+
+# Doom/Package generated
+auto-save-list/
+tramp/
+
+# AI Assistant folders
+.claude/
+.opencode/
+
+# MacOS (just in case)
+.DS_Store
+
+
+
+

ai.el

@@ -0,0 +1,337 @@
+;;; ai.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-2.5-flash
+                    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-2.5-flash
+    :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))
+
+;;; ============================================================================
+;;; Optional: Add Ollama for local models (commented out by default)
+;;; ============================================================================
+
+;; Uncomment to add Ollama support for local models
+;; (after! gptel
+;;   (gptel-make-ollama "Ollama"
+;;     :host "localhost:11434"
+;;     :stream t
+;;     :models '(qwen2.5-coder:latest
+;;               mistral:latest
+;;               llama3.2:latest)))
+
+;; To make Ollama default, uncomment:
+;; (setq gptel-model 'qwen2.5-coder:latest
+;;       gptel-backend (gptel-make-ollama "Ollama"
+;;                       :host "localhost:11434"
+;;                       :stream t
+;;                       :models '(qwen2.5-coder:latest
+;;                                 mistral:latest)))
+
+;;; ============================================================================
+;;; Helper functions
+;;; ============================================================================
+
+(defun my/gptel-quick-explain-region ()
+  "Quickly explain selected code region."
+  (interactive)
+  (when (use-region-p)
+    (let ((code (buffer-substring-no-properties (region-beginning) (region-end))))
+      (gptel-request code
+        :system "Explain this code concisely in 2-3 sentences."
+        :callback (lambda (response info)
+                    (message "Explanation: %s" response))))))
+
+(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.")))
+
+;; Add keybindings for helper functions
+(map! :leader
+      (:prefix "A"
+       :desc "Quick explain" "e" #'my/gptel-quick-explain-region
+       :desc "Proofread text" "p" #'my/gptel-proofread-region))
+
+;;; 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: Enable auto-revert for files modified by Gemini
+  ;; (global-auto-revert-mode 1)
+
+  ;; 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)))))
+
+;; (use-package! claudemacs
+;;   :defer t
+;;   :commands (claudemacs claudemacs-transient-menu)
+;;   :init
+;;   (setq claudemacs-program "ccr"
+;;         claudemacs-program-switches '("code" "--dangerously-skip-permissions")
+;;         claudemacs-default-tool 'claude
+;;         claudemacs-prefer-projectile-root t)
+;;   :config
+;;   (map! :map prog-mode-map
+;;         "C-c C-e" #'claudemacs-transient-menu)
+;;   (map! :map emacs-lisp-mode-map
+;;         "C-c C-e" #'claudemacs-transient-menu)
+;;   (map! :map text-mode-map
+;;         "C-c C-e" #'claudemacs-transient-menu)
+;;   (after! python
+;;     (map! :map python-base-mode-map
+;;           "C-c C-e" #'claudemacs-transient-menu))
+;;   (after! eat
+;;     (setq eat-term-scrollback-size 400000)
+;;     (add-hook 'eat-mode-hook
+;;               (lambda ()
+;;                 (setq-local show-trailing-whitespace nil))))
+;;   (map! :leader
+;;         (:prefix ("C" . "claude-code")
+;;          :desc "Claudemacs menu" "E" #'claudemacs-transient-menu)))

config.el

@@ -1,320 +1,19 @@
 ;;; $DOOMDIR/config.el -*- lexical-binding: t; -*-
 
-(setq doom-theme 'doom-one)
+;; Load modular configuration files
+(load! "security")
+(load! "core")
+(load! "development")
+(load! "org")
+(load! "ai")
+(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/")
+;; Keybinding to open inbox.el
-
+(map! "C-c i" #'(lambda () (interactive) (find-file (expand-file-name "inbox.el" doom-user-dir))))
-(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 "dingfengwong@gmail.com"))
-
-(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
-                  )))

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.el

@@ -0,0 +1,151 @@
+;;; development.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)
+
+  )
+
+;; 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
+        ))
+
+;; Haskell LSP uses HLS by default in Doom; removed outdated fourmolu config
+
+(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\\'"
+  :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)))
+
+(after! lsp-clangd
+  (setq lsp-clients-clangd-executable "clangd")
+  (setq lsp-clients--clangd-default-executable "clangd")
+  (setq lsp-clangd-binary-path "clangd"))
+
+;; Justfile mode (psibi/justl.el)
+(use-package! justl
+  :config
+  (map! :n "e" 'justl-exec-recipe))

inbox.el

@@ -0,0 +1,5 @@
+;;; inbox.el -*- lexical-binding: t; -*-
+
+;; Use this file for new packages and configuration snippets
+;; before sorting them into their proper places.
+

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
@@ -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 "dingfengwong@gmail.com"))
+
+(after! auth-source
+  (setq auth-sources '("~/.authinfo.gpg")))
+
+(setq epa-file-cache-passphrase-for-symmetric-encryption t)

theme.el

@@ -0,0 +1,24 @@
+;;; theme.el -*- lexical-binding: t; -*-
+
+;; Configure ewal
+(use-package! ewal
+  :init
+  (setq 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
+  :config
+  ;; (load-theme 'ewal-doom-one t)
+  ;;(enable-theme 'ewal-doom-one)
+  )
+
+;; Set the theme to ewal-doom-one
+;; (setq doom-theme 'ewal-doom-one)
+(load-theme 'doom-one t)
+(setq doom-theme 'doom-one)
+
+;; Previous base16 config (commented out)
+;; (setq base16-distinct-fringe-background t
+;;       base16-highlight-mode-line 'box)
+;; (setq doom-theme 'base16-default-dark)