Add org layer to Spacemacs (minor cleanup)

emacs/.spacemacs

@@ -43,17 +43,14 @@ This function should only modify configuration layer settings."
      (auto-completion :variables
                    auto-completion-return-key-behavior 'complete
                    auto-completion-tab-key-behavior 'cycle)
-     ;; better-defaults
      emacs-lisp
      git
      markdown
-     html
-     ;; org
+     (org :variables org-projectile-file "TODOs.org")
      (shell :variables
              shell-default-height 30
              shell-default-position 'bottom
              shell-default-shell 'eshell)
-     ;; spell-checking
      syntax-checking
      (version-control :variables
                        version-control-diff-tool 'diff-hl
@@ -71,10 +68,10 @@ This function should only modify configuration layer settings."
      spacemacs-layouts
      dap
      spacemacs-project
-     (python :variables
-             python-backend 'anaconda
-             python-test-runner 'pytest
-             python-enable-yapf-format-on-save t)
+     ;; (python :variables
+             ;; python-backend 'anaconda
+             ;; python-test-runner 'pytest
+             ;; python-enable-yapf-format-on-save t)
      yaml
      latex
      pandoc
@@ -102,6 +99,9 @@ This function should only modify configuration layer settings."
     treemacs
     lsp-treemacs
     rtags
+    company-rtags
+    flycheck-rtags
+    ivy-rtags
   )
 
    ;; Defines the behaviour of Spacemacs when installing packages.
@@ -491,16 +491,19 @@ before packages are loaded."
     (smartparens-global-mode t)
     (show-smartparens-global-mode +1)
     (add-hook 'after-init-hook 'global-company-mode)
-    (add-to-list 'auto-mode-alist '("\\.tpp\\'" . c++-mode))
+    ; Force Vertical Window spawn
     (setq split-height-threshold nil)
     (setq split-width-threshold 0)
+    ; Function Keybindings
     (global-set-key [f3] 'other-window)
     (global-set-key [f4] 'ivy-switch-buffer)
-    (global-set-key [f5] 'delete-window)
+    (global-set-key [f5] 'delete-other-windows)
     (global-set-key [f6] 'counsel-recentf)
     (windmove-default-keybindings)
-    (load-file "~/.emacs.d/private/recentf-ext.el"); Add dired in recentf
-    (setq compilation-finish-function ; Close compilation buffer automatically
+    ; Add dired in recentf
+    (load-file "~/.emacs.d/private/recentf-ext.el")
+    ; Close compilation buffer automatically
+    (setq compilation-finish-function
           (lambda (buf str)
             (if (null (string-match ".*exited abnormally.*" str))
                 ;;no errors, make the compilation window go away in a few seconds
@@ -512,15 +515,24 @@ before packages are loaded."
     (setq magit-repository-directories
           '(("/home/coolneng/Documents/Uni/" . 6)
             ("/home/coolneng/.dotfiles/" . 0)))
-    (setq lsp-ui-doc-enable nil) ; disable lsp-ui-doc
+    ; Disable lsp-ui-doc
+    (setq lsp-ui-doc-enable nil)
     ; Modeline settings
     (doom-modeline-mode t)
     (setq doom-modeline-height 20)
     (setq doom-modeline-buffer-encoding 'nil)
     (setq doom-modeline-major-mode-icon 'nil)
-    ; Select mode for some extensions
+    ; Default mode for some file extensions
+    (add-to-list 'auto-mode-alist '("\\.tpp\\'" . c++-mode))
     (add-to-list 'auto-mode-alist '("\\.aiml\\'" . web-mode))
     (add-to-list 'auto-mode-alist '("\\.latex\\'" . latex-mode))
+    ; Add TODO files to the org-agenda
+    (with-eval-after-load 'org-agenda
+      (require 'org-projectile)
+      (mapcar '(lambda (file)
+                 (when (file-exists-p file)
+                   (push file org-agenda-files)))
+              (org-projectile-todo-files)))
     )
 
 ;; Do not write anything past this comment. This is where Emacs will
@@ -565,7 +577,7 @@ This function is called at the very end of Spacemacs initialization."
  '(objed-cursor-color "#e45649")
  '(package-selected-packages
    (quote
-    (mmm-mode yapfify yaml-mode xterm-color which-key wgrep web-mode use-package tagedit smex smeargle smartparens slim-mode shell-pop scss-mode sass-mode pyvenv pytest pyenv-mode py-isort pug-mode pip-requirements persp-mode pcre2el pandoc-mode ox-pandoc ht orgit org-plus-contrib multi-term markdown-toc markdown-mode magit-gitflow magit-popup magit macrostep live-py-mode ivy-hydra insert-shebang hydra lv hy-mode dash-functional helm-make haml-mode gitignore-mode gitconfig-mode gitattributes-mode git-timemachine git-messenger git-link git-gutter-fringe+ git-gutter-fringe fringe-helper git-gutter+ git-gutter gh-md fuzzy flycheck-pos-tip pos-tip flycheck flx fish-mode eyebrowse exec-path-from-shell transient git-commit with-editor evil-escape goto-chg eshell-z eshell-prompt-extras esh-help emmet-mode elisp-slime-nav doom-modeline shrink-path disaster diminish diff-hl cython-mode counsel-projectile projectile pkg-info epl counsel swiper ivy company-web web-completion-data company-statistics company-shell company-emacs-eclim eclim company-c-headers company-auctex company-anaconda company cmake-mode clang-format bind-map bind-key auto-yasnippet yasnippet auto-compile packed async anaconda-mode pythonic f s all-the-icons memoize ace-window avy ac-ispell auto-complete popup doom-themes dash)))
+    (toc-org org-projectile org-category-capture org-present org-pomodoro alert log4e gntp org-mime org-download org-cliplink org-bullets org-brain gnuplot evil-org yapfify yaml-mode xterm-color which-key wgrep web-mode use-package tagedit smex smeargle smartparens slim-mode shell-pop scss-mode sass-mode pyvenv pytest pyenv-mode py-isort pug-mode pip-requirements persp-mode pcre2el pandoc-mode ox-pandoc ht orgit org-plus-contrib multi-term markdown-toc markdown-mode magit-gitflow magit-popup magit macrostep live-py-mode ivy-hydra insert-shebang hydra lv hy-mode dash-functional helm-make haml-mode gitignore-mode gitconfig-mode gitattributes-mode git-timemachine git-messenger git-link git-gutter-fringe+ git-gutter-fringe fringe-helper git-gutter+ git-gutter gh-md fuzzy flycheck-pos-tip pos-tip flycheck flx fish-mode eyebrowse exec-path-from-shell transient git-commit with-editor evil-escape goto-chg eshell-z eshell-prompt-extras esh-help emmet-mode elisp-slime-nav doom-modeline shrink-path disaster diminish diff-hl cython-mode counsel-projectile projectile pkg-info epl counsel swiper ivy company-web web-completion-data company-statistics company-shell company-emacs-eclim eclim company-c-headers company-auctex company-anaconda company cmake-mode clang-format bind-map bind-key auto-yasnippet yasnippet auto-compile packed async anaconda-mode pythonic f s all-the-icons memoize ace-window avy ac-ispell auto-complete popup doom-themes dash)))
  '(pdf-view-midnight-colors (quote ("#655370" . "#fbf8ef")))
  '(safe-local-variable-values
    (quote