refactor(config/nvim): move pack.add declarations into individual plugin files

The monolithic vim.pack.add() table in init.lua was removed and each
plugin/*.lua file now declares its own dependencies via vim.pack.add()
at the top. tools.lua was decomposed into per-plugin files (cmake.lua,
jupynvim.lua, just.lua, kulala.lua, mise.lua, neogit.lua, sshfs.lua,
trouble.lua, undotree.lua, zoxide.lua) each with their own config and
keymaps. This makes plugin files self-contained and easier to maintain.

config/nvim/plugin/orgmode.lua

@@ -1,4 +1,8 @@
-
+vim.pack.add({
+    { src = 'https://github.com/SjB/orgmode', version = 'sjb-wip' }, 
+    { src = 'https://github.com/chipsenkbeil/org-roam.nvim' },
+    { src = 'https://github.com/akinsho/org-bullets.nvim' },
+})
 require('orgmode').setup({
     ui = {
         input = {