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/treesitter.lua

@@ -1,3 +1,12 @@
+vim.pack.add({
+    { src = 'https://github.com/nvim-treesitter/nvim-treesitter', version = 'main' },
+    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-context' },
+    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-context' },
+    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-textobjects', version = 'main' },
+    { src = 'https://github.com/romus204/tree-sitter-manager.nvim' },
+    { src = 'https://github.com/JoosepAlviste/nvim-ts-context-commentstring' },
+})
+
 require("tree-sitter-manager").setup({
     -- Default Options
     -- ensure_installed = {}, -- list of parsers to install at the start of a neovim session