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/init.lua

@@ -114,96 +114,14 @@ vim.filetype.add({
 })
 
 vim.pack.add({
-    { src = 'https://github.com/3rd/image.nvim' },
-	{ src = "https://github.com/folke/snacks.nvim" },
-    { src = "https://github.com/folke/trouble.nvim" },
-    { src = "https://github.com/olimorris/codecompanion.nvim" },
-    { src = 'https://github.com/Civitasv/cmake-tools.nvim' },
-    { src = 'https://github.com/Davidyz/VectorCode' },
-    { src = 'https://github.com/Glhou/jjsigns.nvim', version = 'fix/skip-extra-lines' },
-    { src = 'https://github.com/HakonHarnes/img-clip.nvim' },
-    { src = 'https://github.com/JoosepAlviste/nvim-ts-context-commentstring' },
-    { src = 'https://github.com/L3MON4D3/LuaSnip' },
-    { src = 'https://github.com/MeanderingProgrammer/render-markdown.nvim' },
-    { src = 'https://github.com/MeanderingProgrammer/render-markdown.nvim' },
     { src = 'https://github.com/MunifTanjim/nui.nvim' },
-    { src = 'https://github.com/NeogitOrg/neogit' },
-    { src = 'https://github.com/PhantomYdn/fabric-ai.nvim' },
-    { src = 'https://github.com/Saecki/crates.nvim' },
-    { src = 'https://github.com/Saghen/blink.cmp', version = vim.version.range('1.*') },
-    { src = 'https://github.com/SjB/orgmode', version = 'sjb-wip' }, 
     { src = 'https://github.com/SmiteshP/nvim-navic' },
-    { src = 'https://github.com/WhoIsSethDaniel/mason-tool-installer.nvim' },
-    { src = 'https://github.com/akinsho/org-bullets.nvim' },
-    { src = 'https://github.com/akinsho/toggleterm.nvim' },
-    { src = 'https://github.com/SjB/codecompanion-agentskills.nvim', version = 'support_disable_model_invocation_flag' },
-    { src = 'https://github.com/carlos-algms/agentic.nvim' },
-    { src = 'https://github.com/chipsenkbeil/org-roam.nvim' },
-    { src = 'https://github.com/christoomey/vim-tmux-navigator' },
---    { src = 'https://github.com/copilotlsp-nvim/copilot-lsp' },
     { src = 'https://github.com/esmuellert/codediff.nvim' },
-    { src = 'https://github.com/fang2hou/blink-copilot' },
-    { src = 'https://github.com/folke/flash.nvim' },
-    { src = 'https://github.com/folke/persistence.nvim' },
     { src = 'https://github.com/folke/todo-comments.nvim' },
-    { src = 'https://github.com/folke/which-key.nvim' },
-    { src = 'https://github.com/franco-ruggeri/codecompanion-spinner.nvim' },
-    { src = 'https://github.com/hat0uma/csvview.nvim' },
-    { src = 'https://github.com/hedyhli/outline.nvim' },
-    { src = 'https://github.com/iamcco/markdown-preview.nvim' },
     { src = 'https://github.com/j-hui/fidget.nvim' },
-    { src = 'https://github.com/jay-babu/mason-nvim-dap.nvim' },
-    { src = 'https://github.com/julienvincent/hunk.nvim' },
-    { src = 'https://github.com/lervag/vimtex' },
-    { src = 'https://github.com/lewis6991/gitsigns.nvim' },
-    { src = 'https://github.com/mbbill/undotree' },
-    { src = 'https://github.com/SjB/meow.review.nvim', version = 'fix-invalid-buffer-id' },
-    { src = 'https://github.com/mfussenegger/nvim-ansible' },
-    { src = 'https://github.com/mfussenegger/nvim-dap' },
-    { src = 'https://github.com/mistweaverco/kulala.nvim' },
-    { src = 'https://github.com/moyiz/blink-emoji.nvim' },
-    { src = 'https://github.com/neovim/nvim-lspconfig' },
     { src = 'https://github.com/norcalli/nvim-colorizer.lua' },
     { src = 'https://github.com/nvim-lua/plenary.nvim' }, 
-    { src = 'https://github.com/nvim-lualine/lualine.nvim' },
-    { src = 'https://github.com/nvim-mini/mini.ai' },
-    { src = 'https://github.com/nvim-mini/mini.align' },
-    { src = 'https://github.com/nvim-mini/mini.bracketed' },
-    { src = 'https://github.com/nvim-mini/mini.extra' },
-    { src = 'https://github.com/nvim-mini/mini.files' },
-    { src = 'https://github.com/nvim-mini/mini.hipatterns' },
-    { src = 'https://github.com/nvim-mini/mini.move' },
-    { src = 'https://github.com/nvim-mini/mini.operators' },
-    { src = 'https://github.com/nvim-mini/mini.sessions' },
-    { src = 'https://github.com/nvim-mini/mini.splitjoin' },
-    { src = 'https://github.com/nvim-mini/mini.surround' },
     { src = 'https://github.com/nvim-neotest/nvim-nio' },
-    { src = 'https://github.com/nvim-pack/nvim-spectre' },
     { src = 'https://github.com/nvim-tree/nvim-web-devicons' },
-    { 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/otavioschwanck/arrow.nvim' },
-    { src = 'https://github.com/rafamadriz/friendly-snippets' },
-    { src = 'https://github.com/rafikdraoui/jj-diffconflicts' },
-    { src = 'https://github.com/ravitemer/codecompanion-history.nvim' },
-    { src = 'https://github.com/ravitemer/codecompanion-history.nvim' },
-    { src = 'https://github.com/rcarriga/nvim-dap-ui' },
-    { src = 'https://github.com/salkin-mada/openscad.nvim' },
-    { src = 'https://github.com/sheng-tse/jupynvim' },
-    { src = 'https://github.com/sindrets/diffview.nvim' },
-    { src = 'https://github.com/stevearc/conform.nvim' },
-    { src = 'https://github.com/stevearc/overseer.nvim' },
-    { src = 'https://github.com/stevearc/quicker.nvim' },
-    { src = 'https://github.com/ten3roberts/window-picker.nvim' },
-    { src = 'https://github.com/thunder-coding/zincoxide' },
-    { src = 'https://github.com/ttgrules/cc-adapter-copilot-cli-acp' },
-    { src = 'https://github.com/uhs-robert/sshfs.nvim' },
-    { src = 'https://github.com/utilyre/barbecue.nvim' },
-    { src = 'https://github.com/williamboman/mason-lspconfig.nvim' },
-    { src = 'https://github.com/williamboman/mason.nvim' },
-    { src = 'https://github.com/zbirenbaum/copilot.lua' },
-    { src = 'https://plugins.ejri.dev/mise.nvim' },
 })
+