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/persistence.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/folke/persistence.nvim' },
+})
+
 require("persistence").setup({
   dir = vim.fn.expand(vim.fn.stdpath("state") .. "/sessions/"), -- directory where session files are saved
   options = { "buffers", "curdir", "tabpages", "winsize" }, -- sessionoptions used when saving sessions