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/codecompanion.lua

@@ -1,3 +1,10 @@
+vim.pack.add({
+    { src = "https://github.com/olimorris/codecompanion.nvim" },
+    { src = 'https://github.com/Davidyz/VectorCode' },
+    { src = 'https://github.com/SjB/codecompanion-agentskills.nvim', version = 'support_disable_model_invocation_flag' },
+    { src = 'https://github.com/franco-ruggeri/codecompanion-spinner.nvim' },
+    { src = 'https://github.com/ravitemer/codecompanion-history.nvim' },
+})
 
 vim.keymap.set({'n', 'v'}, '<leader>mct', '<cmd>CodeCompanionChat Toggle<cr>',  { noremap = true, silent = true, desc = "CC Toggle" })
 vim.keymap.set({'n', 'v'}, '<leader>mca', '<cmd>CodeCompanionActions<cr>',  { noremap = true, silent = true, desc = "CC Action" })